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Stennett CA, France M, Shardell M, Robbins SJ, Brown SE, Johnston ED, Mark K, Ravel J, Brotman RM. Longitudinal profiles of the vaginal microbiota of pre-, peri-, and postmenopausal women: preliminary insights from a secondary data analysis. Menopause 2024; 31:537-545. [PMID: 38787353 DOI: 10.1097/gme.0000000000002358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
OBJECTIVE Menopause is often accompanied by lowered Lactobacillus spp. relative abundance and increased abundance of diverse anaerobic/aerobic bacteria in the vaginal microbiota due in part to declines in estrogen. These microbiota are associated with urogenital symptoms and infections. In premenopause, vaginal microbiota can fluctuate rapidly, particularly with menstrual cycles and sexual activity; however, the longitudinal dynamics of vaginal microbiota are understudied in peri- and postmenopause. We described vaginal community stability across reproductive stages. METHODS Pre- (n = 83), peri- (n = 8), and postmenopausal (n = 11) participants provided twice-weekly mid-vaginal samples (total, 1,556; average, 15 per participant) over 8 weeks in an observational study. Composition of the vaginal microbiota was characterized by 16S rRNA gene amplicon sequencing, and a community state type (CST) was assigned to each sample. Clustering of longitudinal CST profiles, CST transition rates, duration of low-Lactobacillus/high bacterial diversity CSTs, and other metrics of bacterial community dynamics were assessed across reproductive stages. RESULTS The proportion of participants with longitudinal CST profiles characterized by low-Lactobacillus CSTs was similar among pre- (38.6%), peri- (37.5%), and postmenopausal (36.4%) participants (P = 0.69). CST transition rates between consecutive samples were 21.1%, 16.7%, and 14.6% for pre-, peri-, and postmenopausal participants, respectively (P = 0.49). Low-Lactobacillus CST tended to persist for at least 4 weeks, irrespective of reproductive stage. CONCLUSIONS Findings from this small yet frequently sampled cohort revealed vaginal bacterial fluctuations over 8 weeks that were similar across reproductive stages. Larger and longer-term studies based on these preliminary data could provide insights into the influence of microbiota dynamics on urogenital outcomes during menopause.
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Affiliation(s)
| | | | | | | | | | - Elizabeth D Johnston
- Department of Obstetrics and Gynecology, University of Maryland School of Medicine, Baltimore, MD
| | - Katrina Mark
- Department of Obstetrics and Gynecology, University of Maryland School of Medicine, Baltimore, MD
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Scheible K, Beblavy R, Sohn MB, Qui X, Gill AL, Narvaez-Miranda J, Brunner J, Miller RK, Barrett ES, O’Connor TG, Gill SR. Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589254. [PMID: 38645042 PMCID: PMC11030453 DOI: 10.1101/2024.04.12.589254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Composition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Identifying the sources of individual differences in the vaginal microbiome is therefore of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual's experience of affective symptoms and stress exposure. Data were based on a prospective longitudinal study of a diverse and medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34-40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community state types (CST1-3) based on dissimilarity of vaginal microbiota composition. Results indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CST3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CST1-3 and individual taxa, including biosynthetic pathways for the neuroactive metabolites, serotonin and dopamine. With the exception of bioavailable testosterone, no significant associations were found between symptoms- and stress-related biomarkers and CSTs. Our results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.
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Affiliation(s)
- Kristin Scheible
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Robert Beblavy
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Michael B. Sohn
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Xing Qui
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Ann L. Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Janiret Narvaez-Miranda
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jessica Brunner
- Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Richard K. Miller
- Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Emily S. Barrett
- Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Tom G. O’Connor
- Department of Psychiatry, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Wynne Center for Family Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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Kensara A, Saito H, Mongodin EF, Masri R. Microbiological profile of peri-implantitis: Analyses of peri-implant microbiome. J Prosthodont 2024; 33:330-339. [PMID: 37527556 DOI: 10.1111/jopr.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/27/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023] Open
Abstract
PURPOSE To characterize the microbiome composition in peri-implant pocket of peri-implantitis and peri-implant sulcus controls using 16S rRNA gene sequencing. MATERIALS AND METHODS In this controlled clinical cross-sectional study, 23 subjects with control implants (n = 14) and diseased implants (peri-implantitis, n = 21) were included. The peri-implant pocket/sulcus was sampled and used to extract DNA and amplify the 16S rRNA gene using universal primers targeting the V3-V4 regions. The resulting 16S PCR amplicons were sequenced on Illumina MiSeq, and the sequences were processed using DADA2 and the Human Oral Microbiome Database (HOMD) as references. Alpha and Beta diversity, as well as core microbiome and differential abundance analyses, were performed using the MicrobiomeAnalyst workflow. RESULTS There were no significant differences in microbial diversity between control implants and implants with peri-implantitis (Shannon p = 0.82). Overall bacterial community structure assessed through beta diversity analysis was also not significantly different between the two groups (p = 0.18). However, high levels of Gram-negative bacteria were detected in peri-implant pockets compared to the control sulcus. Abundant species in peri-implantitis were Capnocytophaga leadbetteri, Treponema maltophilum, Peptostreptococcus, Neisseria, P. gingivalis, and Porphyromonas endodontali, Lactococcus lactis and Filifactor alocis (p < 0.05). Gram-positive bacteria such as Streptococcus salivaris, Prevotella melaninogenica, L. wadei, and Actinomyces spp. serve were more abundant in peri-implant control sulcus. CONCLUSIONS Peri-implant sulcus in control implants harbors predominantly Gram-positive bacteria, whereas pockets of implants with peri-implantitis harbor predominantly Gram-negative bacteria.
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Affiliation(s)
- Anmar Kensara
- Department of Restorative Dentistry, College of Dentistry, Umm Al Qura University, Makkah, Saudi Arabia
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Hanae Saito
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, Maryland, USA
- Division of Lung Diseases, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Radi Masri
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
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Mauck C, Thurman A, Jensen JT, Schreiber CA, Baker J, Hou MY, Chavoustie S, Dart C, Wu H, Ravel J, Gajer P, Herold BC, Jacot T, Zack N, Hatheway J, Friend D. Safety testing of Ovaprene: An investigational nonhormonal monthly vaginal contraceptive. Contraception 2024:110440. [PMID: 38552818 DOI: 10.1016/j.contraception.2024.110440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVES Evaluate the safety of Ovaprene, an investigational nonhormonal vaginal contraceptive designed for monthly use. STUDY DESIGN Open-label, multicenter study enrolling heterosexually-active women with previous permanent contraception who underwent assessments during five menstrual cycles: baseline postcoital test cycle, diaphragm postcoital test cycle, Ovaprene safety cycle, and two Ovaprene postcoital test cycles. Safety outcomes included treatment-emergent adverse events, systemic laboratory findings, pelvic examinations, colposcopies, Nugent scores, determination of community state types of vaginal microbiota, and anti-Escherichia coli activity and inflammatory markers in cervicovaginal fluids. RESULTS We enrolled 38 participants. Of these, 33 used Ovaprene and completed 77 Ovaprene cycles. The most common product-related urogenital treatment-emergent adverse events were bacterial vaginosis and vaginal odor. The frequency of transitioning from Lactobacillus-dominated community state type to community state type IV (not Lactobacillus-dominated) was similar before Ovaprene use and afterwards. Mean Nugent scores were <4 at each visit without a discernible upward trend. Inflammatory markers showed wide variation but no upward trend, and E. coli inhibitory activity of cervical secretions did not change. We found no Staphylococcus aureus, the causative agent in toxic shock syndrome, on used Ovaprenes or in vaginal samples. No clinically important changes in systemic laboratory findings, pelvic examinations, or colposcopies occurred during Ovaprene use. CONCLUSIONS Ovaprene use did not result in cervicovaginal irritation or adverse effects on resident vaginal microbiota and did not impact transitions from a Lactobacillus-dominated community state type to community state type IV. IMPLICATIONS The finding that the use of Ovaprene, an investigational monthly user-controlled nonhormonal vaginal contraceptive, does not appear to result in adverse changes in vaginal health during short-term use supports further evaluation of the contraceptive potential of the device.
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Affiliation(s)
| | - Andrea Thurman
- Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Jeffrey T Jensen
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, United States
| | - Courtney A Schreiber
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, United States
| | - Jeff Baker
- Clinical Research Prime, Idaho Falls, ID, United States
| | - Melody Y Hou
- Department of Obstetrics and Gynecology, University of California Davis, Sacramento, CA, United States
| | - Steven Chavoustie
- Segal Institute for Clinical Research Inc., Miami, FL, United States
| | - Clint Dart
- Premier Research, Morrisville, NC, United States
| | - Hongsheng Wu
- Premier Research, Morrisville, NC, United States
| | - Jacques Ravel
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, United States
| | - Pawel Gajer
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, United States
| | - Betsy C Herold
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Terry Jacot
- Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Nadene Zack
- Daré Bioscience, Inc., San Diego, CA, United States
| | | | - David Friend
- Daré Bioscience, Inc., San Diego, CA, United States
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Yin PK, Xiao H, Yang ZB, Yang DS, Yang YH. Shotgun metagenomics reveals the gut microbial diversity and functions in Vespa mandarinia (Hymenoptera: Vespidae) at multiple life stages. Front Microbiol 2024; 15:1288051. [PMID: 38529182 PMCID: PMC10961340 DOI: 10.3389/fmicb.2024.1288051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/12/2024] [Indexed: 03/27/2024] Open
Abstract
Wasps play important roles as predators and pollinators in the ecosystem. The Jingpo minority residing in Yunnan Province, China, has a traditional practice of using wine infused with mature wasps as a customary remedy for managing rheumatoid arthritis. The larva of the wasp is also a tasteful folk dish that has created a tremendous market. There is a paucity of survival knowledge, which has greatly restricted their potential applications in food and healthcare. Recent research has highlighted the importance of gut microbiota in insect growth. Nevertheless, there is still a lack of understanding regarding the composition, changes, and functions of the gut microbiota in Vespa mandarinia during development. In this research, the gut microbiota were investigated across three growth stages of Vespa mandarinia using a metagenomic technology. The result revealed that there are significant variations in the proportion of main gut microbes during the metamorphosis of Vespa mandarinia. Tenericutes were found to dominate during the larval stage, while Proteobacteria emerged as the dominant group post-pupation. Through a comprehensive analysis of the gut microbiota metagenome, this study revealed functional differences in the wasp gut microbiota at various growth stages. During the larval stage, the gut microbiota plays a central role in promoting metabolism. Following pupation, the gut microbiota exhibited diversified functions, likely due to the complex environments and diverse food sources encountered after metamorphosis. These functions included amino acid metabolism, compound degradation, and defense mechanisms. This research provides an extensive dataset on the gut microbiota during the metamorphosis of Vespa mandarinia, contributing to a deeper understanding of the influence of gut microbiota on wasp growth. Furthermore, this study uncovers a unique microbial treasure within insect guts, which is important for advancing the application of wasps in the fields of food and medicine.
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Affiliation(s)
- Peng-Kai Yin
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Huai Xiao
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Zhi-Bin Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Da-Song Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Yin-He Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
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Robbins SJ, Brown SE, Stennett CA, Tuddenham S, Johnston ED, Wnorowski AM, Ravel J, He X, Mark KS, Brotman RM. Uterine fibroids and longitudinal profiles of the vaginal microbiota in a cohort presenting for transvaginal ultrasound. PLoS One 2024; 19:e0296346. [PMID: 38315688 PMCID: PMC10843103 DOI: 10.1371/journal.pone.0296346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/11/2023] [Indexed: 02/07/2024] Open
Abstract
Bacterial vaginosis, characterized in part by low levels of vaginal Lactobacillus species, has been associated with pro-inflammatory cytokines which could fuel uterine fibroid development. However, prior work on the associations between uterine fibroids and vaginal bacteria is sparse. Most studies have focused on assessment of individual taxa in a single sample. To address research gaps, we sought to compare short, longitudinal profiles of the vaginal microbiota in uterine fibroid cases versus controls with assessment for hormonal contraceptives (HCs), a possible confounder associated with both protection from fibroid development and increases in Lactobacillus-dominated vaginal microbiota. This is a secondary analysis of 83 reproductive-age cisgender women who presented for transvaginal ultrasound (TVUS) and self-collected mid-vaginal swabs daily for 1-2 weeks before TVUS (Range: 5-16 days, n = 697 samples). Sonography reports detailed uterine fibroid characteristics (N = 21 cases). Vaginal microbiota was assessed by 16S rRNA gene amplicon sequencing and longitudinal microbiota profiles were categorized by hierarchical clustering. We compared longitudinal profiles of the vaginal microbiota among fibroid cases and controls with exact logistic regression. Common indications for TVUS included pelvic mass (34%) and pelvic pain (39%). Fibroid cases tended to be older and report Black race. Cases less often reported HCs versus controls (32% vs. 58%). A larger proportion of cases had low-Lactobacillus longitudinal profiles (48%) than controls (34%). In unadjusted analysis, L. iners-dominated and low-Lactobacillus profiles had higher odds of fibroid case status compared to other Lactobacillus-dominated profiles, however these results were not statistically significant. No association between vaginal microbiota and fibroids was observed after adjusting for race, HC and menstruation. Results were consistent when number of fibroids were considered. There was not a statistically significant association between longitudinal profiles of vaginal microbiota and uterine fibroids after adjustment for common confounders; however, the study was limited by small sample size.
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Affiliation(s)
- Sarah J. Robbins
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Sarah E. Brown
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Christina A. Stennett
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Susan Tuddenham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabeth D. Johnston
- Department of Obstetrics and Gynecology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Amelia M. Wnorowski
- Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Xin He
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, Maryland, United States of America
| | - Katrina S. Mark
- Department of Obstetrics and Gynecology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca M. Brotman
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
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Guan X, Cheng P, Wei R, Li J, Jiao S, Zhao Z, Chen H, Liu Z, Jiang Z, Zheng Z, Zou S, Wang X. Enlarged tumour-draining lymph node with immune-activated profile predict favourable survival in non-metastatic colorectal cancer. Br J Cancer 2024; 130:31-42. [PMID: 37957322 PMCID: PMC10781685 DOI: 10.1038/s41416-023-02473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND The tumour-draining lymph node (TDLN) plays a pivotal role in the suppression of malignant tumour, however, the immunological profile and prognostic differences between large TDLN (L-TDLN) and small TDLN (S-TDLN) in colorectal cancer (CRC) remain unclear. METHODS We conducted a study using data from the Chinese National Cancer Center (CNCC) database, identifying 837 CRC patients with non-metastatic TDLN, and categorised them into L-TDLN and S-TDLN groups. The long-term survival outcomes and adjuvant therapy efficacy were compared between the two groups. Furthermore, we evaluated the differences in immune activation status and immune cell subsets between patients in L-TDLN and S-TDLN groups by RNA sequencing and immunohistochemical (IHC) staining. RESULTS Patients with L-TDLN demonstrated better long-term outcomes compared to those with S-TDLN. Among patients with L-TDLN, there was no significant difference in long-term outcomes between those who received adjuvant chemotherapy and those who did not. The RNA sequencing data revealed a wealth of immune-activating pathways explored in L-TDLN. Furthermore, IHC analysis demonstrated higher numbers of CD3+ and CD8 + T cells in L-TDLN and the corresponding CRC lesions, as compared to patients with S-TDLN. CONCLUSION Enlarged TDLN exhibited an activated anti-tumour immune profile and may serve as an indicator for favourable survival in non-metastatic CRC.
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Affiliation(s)
- Xu Guan
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Pu Cheng
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ran Wei
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jiangtao Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Jiao
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Zhixun Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haipeng Chen
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Jiang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhaoxu Zheng
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Shuangmei Zou
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xishan Wang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
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Gigi RMS, Mdingi MM, Jung H, Claassen-Weitz S, Bütikofer L, Klausner JD, Muzny CA, Taylor CM, van de Wijgert JHHM, Peters RPH, Low N. Genital tract infections, the vaginal microbiome and gestational age at birth among pregnant women in South Africa: a cohort study protocol. BMJ Open 2023; 13:e081562. [PMID: 38154893 PMCID: PMC10759125 DOI: 10.1136/bmjopen-2023-081562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/06/2023] [Indexed: 12/30/2023] Open
Abstract
INTRODUCTION Preterm birth complications are the most common cause of death in children under 5 years. The presence of multiple microorganisms and genital tract inflammation could be the common mechanism driving early onset of labour. South Africa has high levels of preterm birth, genital tract infections and HIV infection among pregnant women. We plan to investigate associations between the presence of multiple lower genital tract microorganisms in pregnancy and gestational age at birth. METHODS AND ANALYSIS This cohort study enrols around 600 pregnant women at one public healthcare facility in East London, South Africa. Eligible women are ≥18 years and at <27 weeks of gestation, confirmed by ultrasound. At enrolment and 30-34 weeks of pregnancy, participants receive on-site tests for Chlamydia trachomatis and Neisseria gonorrhoeae, with treatment if test results are positive. At these visits, additional vaginal specimens are taken for: PCR detection and quantification of Trichomonas vaginalis, Candida spp., Mycoplasma genitalium, M. hominis, Ureaplasma urealyticum and U. parvum; microscopy and Nugent scoring; and for 16S ribosomal RNA gene sequencing and quantification. Pregnancy outcomes are collected from a postnatal visit and birth registers. The primary outcome is gestational age at birth. Statistical analyses will explore associations between specific microorganisms and gestational age at birth. To explore the association with the quantity of microorganisms, we will construct an index of microorganism load and use mixed-effects regression models and classification and regression tree analysis to examine which combinations of microorganisms contribute to earlier gestational age at birth. ETHICS AND DISSEMINATION This protocol has approvals from the University of Cape Town Research Ethics Committee and the Canton of Bern Ethics Committee. Results from this study will be uploaded to preprint servers, submitted to open access peer-reviewed journals and presented at regional and international conferences. TRIAL REGISTRATION NUMBER NCT06131749; Pre-results.
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Affiliation(s)
- Ranjana M S Gigi
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Research Unit, Foundation for Professional Development, East London, South Africa
| | - Mandisa M Mdingi
- Research Unit, Foundation for Professional Development, East London, South Africa
| | - Hyunsul Jung
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Lukas Bütikofer
- CTU Bern, Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Jeffrey D Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Janneke H H M van de Wijgert
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Remco P H Peters
- Research Unit, Foundation for Professional Development, East London, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Kensara A, Saito H, Mongodin EF, Masri R. Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants. J Prosthodont 2023; 32:783-792. [PMID: 36691777 DOI: 10.1111/jopr.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
PURPOSE To characterize the microbiome composition within dental implants of peri-implantitis subjects and healthy controls using 16S rRNA gene sequencing. MATERIALS AND METHODS Twenty-three subjects with healthy (n = 11 implants) and diseased (peri-implantitis, n = 21) implants were included in this controlled clinical cross-sectional study. Samples were obtained from internal surfaces of dental implants using sterile paper points for microbiological analysis. DNA was extracted, and the16S rRNA gene was amplified using universal primers targeting the V3-V4 regions. The resulting 16S polymerize chain reaction amplicons were sequenced on Illumina MiSeq, and the sequences were processed using DADA2 and the Human Oral Microbiome Database (HOMD) as references. Alpha and Beta diversity, as well as core microbiome and differential abundance analyses were then performed using the MicrobiomeAnalyst workflow. RESULTS A significant increase in microbial diversity was observed in the internal implant surface of healthy implants compared with the internal surfaces of peri-implantitis (Shannon p = 0.02). Bacterial community structure was significantly different among groups (p = 0.012). High levels of Gram-positive bacteria were detected inside implants with peri-implantitis compared to healthy implants, especially Enterococci. CONCLUSIONS There is a shift in bacterial diversity inside implants with peri-implantitis from the healthy control. The microbial colonization within that space might contribute to the etiology of peri-implant disease.
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Affiliation(s)
- Anmar Kensara
- Department of Restorative Dentistry, College of Dentistry, Umm Al Qura University, Makkah, Saudi Arabia
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Hanae Saito
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Radi Masri
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
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10
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Waetjen LE, Crawford SL, Gajer P, Brooks MM, Gold EB, Reed BD, Hess R, Ravel J. Relationships between the vaginal microbiota and genitourinary syndrome of menopause symptoms in postmenopausal women: the Study of Women's Health Across the Nation. Menopause 2023; 30:1073-1084. [PMID: 37788422 PMCID: PMC10615695 DOI: 10.1097/gme.0000000000002263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
OBJECTIVE To describe vaginal microbiota classified by community state types (CST) in a diverse cohort of postmenopausal women and evaluate relationships among genitourinary syndrome of menopause (GSM) symptoms (vaginal dryness, vulvovaginal irritation, sexual pain, dysuria, urinary urgency), CSTs, estrogen, vaginal maturation index (VMI), and vaginal pH. METHODS In the Study of Women's Health Across the Nation, 1,320 women aged 60.4 to 72.5 years self-collected (2015-2017) vaginal samples analyzed for microbiota composition and structure (CSTs) using 16S rRNA gene amplicon sequencing, VMI, and pH. GSM symptoms were collected with self-administered questionnaires; interviewers elicited estrogen use and measured body mass index. Serum E2 and E1 were measured using high-performance liquid chromatography. We analyzed data using Pearson χ2 tests, analysis of variance, Kruskal-Wallis tests, and binomial logistic regression. RESULTS The most frequently occurring CST was low Lactobacillus species IV-C (49.8%); 36.4% of women had CSTs dominated by Lactobacillus species. More than half of the women with vaginal atrophy biomarkers (VMI <50 and pH >5) had CST IV-C0, whereas women using estrogen or with higher E1 and E2 levels had a higher prevalence of Lactobacillus crispatus -dominated CST I ( P values < 0.001). Sexual pain was associated with atrophy biomarkers and independently associated with Streptococcus species-dominated CST IV-C1 (odds ratio, 2.26; 95% confidence intervals, 1.20-4.23). For all other GSM symptoms, we found no consistent associations with E1 or E2 levels, atrophy biomarkers, or any CST. CONCLUSIONS Although close relationships exist among estrogen, CSTs, VMI, and pH, sexual pain was the only GSM symptom associated with the structure of vaginal microbiota and atrophy biomarkers.
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Affiliation(s)
- L Elaine Waetjen
- From the University of California Davis, School of Medicine, Sacramento, CA
| | - Sybil L Crawford
- Tan Chingfen Graduate School of Nursing, UMass Chan Medical School, Worcester, MA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Maria M Brooks
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA
| | - Ellen B Gold
- From the University of California Davis, School of Medicine, Sacramento, CA
| | - Barbara D Reed
- School of Medicine, University of Michigan, Ann Arbor, MI
| | - Rachel Hess
- University of Utah, School of Medicine, Salt Lake City, UT
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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11
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Jakab S, Bali K, Freytag C, Pataki A, Fehér E, Halas M, Jerzsele Á, Szabó I, Szarka K, Bálint Á, Bányai K. Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance. Animals (Basel) 2023; 13:3223. [PMID: 37893946 PMCID: PMC10603690 DOI: 10.3390/ani13203223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.
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Affiliation(s)
- Szilvia Jakab
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | - Krisztina Bali
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | - Csongor Freytag
- Department of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (C.F.); (K.S.)
| | - Anna Pataki
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
| | - Enikő Fehér
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | | | - Ákos Jerzsele
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary;
| | - István Szabó
- National PRRS Eradication Committee, Keleti Károly u. 24., H-1024 Budapest, Hungary;
| | - Krisztina Szarka
- Department of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (C.F.); (K.S.)
| | - Ádám Bálint
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, H-1143 Budapest, Hungary;
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary;
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12
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Tuddenham S, Shafiq M, Mathad JS, Alexander M, Naik S, Kulkarni V, Deshpande P, Humphrys MS, Holm JB, Khan N, Yadana S, Cheedalla A, Bhosale R, Ghanem KG, Wang T, Wang S, Ma B, Ravel J, Gupta A, Shivakoti R. Association of Pregnancy and HIV Status With Molecular-Bacterial Vaginosis in Indian Women. J Acquir Immune Defic Syndr 2023; 93:422-430. [PMID: 37155962 PMCID: PMC10524256 DOI: 10.1097/qai.0000000000003215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Bacterial vaginosis (BV) is a highly prevalent disorder of the cervicovaginal microbiota. Molecular-BV may put women at increased risk for adverse reproductive and obstetric outcomes. We investigated the association of HIV and pregnancy on the vaginal microbiota and associations with molecular-BV in women of reproductive age from Pune, India. SETTING We studied vaginal samples from N = 170 women, including N = 44 nonpregnant HIV seronegative, N = 56 pregnant seronegative, N = 47 nonpregnant women with HIV (WWH), and N = 23 pregnant WWH, and collected data on clinical, behavioral, and demographic factors. METHODS We used 16S rRNA gene amplicon sequencing to characterize the composition of the vaginal microbiota. We classified the vaginal microbiota of these women into community state types based on bacterial composition and relative abundance and further categorized them into molecular-BV versus Lactobacillus -dominated states. To determine associations between pregnancy and HIV status with outcome of molecular-BV, logistic regression models were used. RESULTS There was a high prevalence of molecular-BV (30%) in this cohort. We found that pregnancy was associated with decreased odds of molecular-BV (adjusted OR = 0.35, 95% CI: 0.14 to 0.87), while HIV was associated with increased odds of molecular-BV (adjusted OR = 2.76, 95% CI: 1.33 to 5.73), even when controlling for multiple relevant factors such as age, number of sexual partners, condom use, and douching. CONCLUSION Larger and longitudinal studies are needed to further characterize molecular-BV and the vaginal microbiota in pregnant women and WWH and relate these factors to infectious, reproductive, and obstetric outcomes. In the long term, these studies may lead to novel microbiota-based therapeutics to improve women's reproductive and obstetric health.
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Affiliation(s)
- Susan Tuddenham
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mehr Shafiq
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Jyoti S. Mathad
- Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Mallika Alexander
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Shilpa Naik
- Department of Obstetrics and Gynecology, Byramjee Jeejeebhoy Government Medical College, Pune, India
| | - Vandana Kulkarni
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Prasad Deshpande
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Mike S. Humphrys
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Johanna B. Holm
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Nawshaba Khan
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Su Yadana
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | | | - Ramesh Bhosale
- Department of Obstetrics and Gynecology, Byramjee Jeejeebhoy Government Medical College, Pune, India
| | - Khalil G. Ghanem
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Tian Wang
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, USA
| | - Shuang Wang
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, USA
| | - Bing Ma
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Amita Gupta
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rupak Shivakoti
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
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13
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Mehta SD, Agingu W, Zulaika G, Nyothach E, Bhaumik R, Green SJ, van Eijk AM, Otieno FO, Phillips-Howard PA, Schneider J. Vaginal Microbial Network Analysis Reveals Novel Taxa Relationships among Adolescent and Young Women with Incident Sexually Transmitted Infection Compared with Those Remaining Persistently Negative over a 30-Month Period. Microorganisms 2023; 11:2035. [PMID: 37630595 PMCID: PMC10459434 DOI: 10.3390/microorganisms11082035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A non-optimal vaginal microbiome (VMB) is typically diverse with a paucity of Lactobacillus crispatus and is often associated with bacterial vaginosis (BV) and sexually transmitted infections (STIs). Although compositional characterization of the VMB is well-characterized, especially for BV, knowledge remains limited on how different groups of bacteria relate to incident STIs, especially among adolescents. In this study, we compared the VMB (measured via 16S ribosomal RNA gene amplicon sequencing) of Kenyan secondary school girls with incident STIs (composite of chlamydia, gonorrhea, and trichomoniasis) to those who remained persistently negative for STIs and BV over 30 months of follow-up. We applied microbial network analysis to identify key taxa (i.e., those with the greatest connectedness in terms of linkages to other taxa), as measured by betweenness and eigenvector centralities, and sub-groups of clustered taxa. VMB networks of those who remained persistently negative reflected greater connectedness compared to the VMB from participants with STI. Taxa with the highest centralities were not correlated with relative abundance and differed between those with and without STI. Subject-level analyses indicated that sociodemographic (e.g., age and socioeconomic status) and behavioral (e.g., sexual activity) factors contribute to microbial network structure and may be of relevance when designing interventions to improve VMB health.
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Affiliation(s)
- Supriya D. Mehta
- Division of Epidemiology & Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL 60612, USA
- Division of Infectious Disease Medicine, College of Medicine, Rush University, Chicago, IL 60612, USA
| | - Walter Agingu
- Nyanza Reproductive Health Society, Kisumu P.O. Box 1764, Kenya
| | - Garazi Zulaika
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK (P.A.P.-H.)
| | | | - Runa Bhaumik
- Division of Epidemiology & Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- Division of Infectious Disease Medicine, College of Medicine, Rush University, Chicago, IL 60612, USA
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL 60612, USA
| | - Anna Maria van Eijk
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK (P.A.P.-H.)
| | | | | | - John Schneider
- Departments of Medicine and Public Health Sciences, School of Medicine, University of Chicago, Chicago, IL 60637, USA;
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14
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Musa J, Maiga M, Green SJ, Magaji FA, Maryam AJ, Okolo M, Nyam CJ, Cosmas NT, Silas OA, Imade GE, Zheng Y, Joyce BT, Diakite B, Morhason-Bello I, Achenbach CJ, Sagay AS, Ujah IAO, Murphy RL, Hou L, Mehta SD. Vaginal microbiome community state types and high-risk human papillomaviruses in cervical precancer and cancer in North-central Nigeria. BMC Cancer 2023; 23:683. [PMID: 37474918 PMCID: PMC10360349 DOI: 10.1186/s12885-023-11187-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND High risk human papillomaviruses (HR-HPV) have a causal role in cervical oncogenesis, and HIV-mediated immune suppression allows HR-HPV to persist. We studied whether vaginal microbiome community state types (CSTs) are associated with high-grade precancer and/or invasive cervical cancer (HSIL/ICC). METHODS This was a cross-sectional study of adult women with cervical cancer screening (CCS) at the Jos University Teaching Hospital (JUTH) in Jos, Nigeria, between January 2020 and February 2022. Cervical swabs underwent HPV genotyping (Anyplex™ II HPV28). Cervico-vaginal lavage (CVL) sample was collected for 16 S rRNA gene amplicon sequencing. We used multivariable logistic regression modelling to assess associations between CSTs and other factors associated with HSIL/ICC. RESULTS We enrolled 155 eligible participants, 151 with microbiome data for this analysis. Women were median age 52 (IQR:43-58), 47.7% HIV positive, and 58.1% with HSIL/ICC. Of the 138 with HPV data, 40.6% were negative for HPV, 10.1% had low-risk HPV, 26.8% had single HR-HPV, and 22.5% had multiple HR-HPV types. The overall prevalence of any HR-HPV type (single and multiple) was 49.3%, with a higher proportion in women with HSIL/ICC (NILM 31.6%, LSIL 46.5%, HSIL 40.8%, and 81.5% ICC; p = 0.007). Women with HIV were more likely to have HSIL/ICC (70.3% vs. 29.7% among women without HIV). In crude and multivariable analysis CST was not associated with cervical pathology (CST-III aOR = 1.13, CST-IV aOR = 1.31). However, in the presence of HR-HPV CST-III (aOR = 6.7) and CST-IV (aOR = 3.6) showed positive association with HSIL/ICC. CONCLUSION Vaginal microbiome CSTs were not significantly associated with HSIL/ICC. Our findings suggest however, that CST could be helpful in identifying women with HSIL/ICC and particularly those with HR-HPV. Characterization of CSTs using point-of-care molecular testing in women with HR-HPV should be studied as an approach to improve early detection and cervical cancer prevention. Future longitudinal research will improve our understanding of the temporal effect of non-optimal CST, HR-HPV, and other factors in cervical cancer development, prevention, and control.
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Affiliation(s)
- Jonah Musa
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Plateau State, Nigeria.
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, USA.
- Center for Global Oncology, Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, USA.
| | - Mamoudou Maiga
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, USA
- Center for Global Oncology, Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, USA
- Center for innovations in Healthcare Technologies, McCormick's School of Biomedical Engineering, Northwestern University, Chicago, IL, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, USA
| | - Francis A Magaji
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Plateau State, Nigeria
| | - Ali J Maryam
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Mark Okolo
- Department of Medical Microbiology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Chuwang J Nyam
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
- Genomics and Postgraduate Core Facility, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Nanma T Cosmas
- Department of Medical Microbiology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Olugbenga A Silas
- Department of Anatomic Pathology and Forensic Medicine, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Godwin E Imade
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Plateau State, Nigeria
- Genomics and Postgraduate Core Facility, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Yinan Zheng
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Brian T Joyce
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Brehima Diakite
- University of Sciences, Technique and Technologies of Bamako, Bamako, Mali
| | - Imran Morhason-Bello
- Department of Obstetrics and Gynecology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Chad J Achenbach
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
- Robert J. Havey MD, Institute for Global Health, Northwestern University, Chicago, IL, USA
| | - Atiene S Sagay
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Plateau State, Nigeria
| | - Innocent A O Ujah
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Plateau State, Nigeria
- Federal University of Health Sciences, Otukpo, Benue State, Nigeria
| | - Robert L Murphy
- Department of Obstetrics and Gynecology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Robert J. Havey MD, Institute for Global Health, Northwestern University, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, USA
- Center for Global Oncology, Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, USA
- Robert H. Lurie Comprehensive Cancer Center, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Supriya Dinesh Mehta
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
- Department of Epidemiology and Biostatistics, Rush University, Chicago, IL, USA
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15
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Brown SE, He X, Shardell MD, Ravel J, Ghanem KG, Zenilman JM, Brotman RM. Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. Sex Transm Infect 2023; 99:156-161. [PMID: 35636931 PMCID: PMC9708945 DOI: 10.1136/sextrans-2022-055459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/01/2022] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Observational studies demonstrate an association between vaginal douching and bacterial vaginosis (BV) characterised by Gram stain. We sought to describe the effect of a douching cessation intervention on the composition and structure of the vaginal microbiota and molecular-BV, a state defined by low levels of Lactobacillus spp evaluated by molecular tools. METHODS 33 women self-collected mid-vaginal swabs twice weekly (982 samples) during a douching observation phase (4 weeks) followed by a douching cessation phase (12 weeks) in a 2005 single crossover pilot study conducted in Baltimore, Maryland. Vaginal microbiota were characterised by 16S rRNA gene amplicon sequencing (V3-V4) and clustered into community state types (CSTs). Conditional logistic regression modelling allowed each participant to serve as their own control. Wilcoxon signed-rank tests were used to evaluate changes in microbiota between phases. Broad-range qPCR assays provided estimates of bacterial absolute abundance per swab in a subsample of seven participants before and after douching. A piecewise linear mixed effects model was used to assess rates of change in bacterial absolute abundance before and after douching. RESULTS There was no statistically significant change in the odds of molecular-BV versus Lactobacillus-dominated CSTs comparing the douching cessation interval to douching observation (adjusted OR 1.77, 95% CI 0.89 to 3.55). Removal of L. iners-dominated CST III from the outcome did not affect the results. There were no significant changes in the relative abundance of four Lactobacillus spp and no meaningful changes in other taxa investigated. There was no significant change in bacterial absolute abundance between a participant's sample collected 3 days prior to and following douching (p=0.46). CONCLUSIONS In this pilot study, douching cessation was not associated with major changes in vaginal microbiota. Douching cessation alone may not durably shift the vaginal microbiota and additional interventions may be needed to restore optimal vaginal microbiota among those who douche.
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Affiliation(s)
- Sarah Elizabeth Brown
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Xin He
- Department of Epidemiology and Biostatistics, University of Maryland at College Park, College Park, Maryland, USA
| | - Michelle D Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Khalil G Ghanem
- Division of Infectious Diseases, Johns Hopkins Medicine School of Medicine, Baltimore, Maryland, USA
| | - Jonathan M Zenilman
- Division of Infectious Diseases, Johns Hopkins Medicine School of Medicine, Baltimore, Maryland, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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16
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Cao Y, Chen X, Shu L, Shi L, Wu M, Wang X, Deng K, Wei J, Yan J, Feng G. Analysis of the correlation between BMI and respiratory tract microbiota in acute exacerbation of COPD. Front Cell Infect Microbiol 2023; 13:1161203. [PMID: 37180432 PMCID: PMC10166817 DOI: 10.3389/fcimb.2023.1161203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
Objective To investigate the distribution differences in the respiratory tract microbiota of AECOPD patients in different BMI groups and explore its guiding value for treatment. Methods Sputum samples of thirty-eight AECOPD patients were collected. The patients were divided into low, normal and high BMI group. The sputum microbiota was sequenced by 16S rRNA detection technology, and the distribution of sputum microbiota was compared. Rarefaction curve, α-diversity, principal coordinate analysis (PCoA) and measurement of sputum microbiota abundance in each group were performed and analyzed by bioinformatics methods. Results 1. The rarefaction curve in each BMI group reached a plateau. No significant differences were observed in the OTU total number or α-diversity index of microbiota in each group. PCoA showed significant differences in the distance matrix of sputum microbiota between the three groups, which was calculated by the Binary Jaccard and the Bray Curtis algorithm. 2. At the phylum level, most of the microbiota were Proteobacteria, Bacteroidetes Firmicutes, Actinobacteria, and Fusobacteria. At the genus level, most were Streptococcus, Prevotella, Haemophilus, Neisseria and Bacteroides. 3. At the phylum level, the abundance of Proteobacteria in the low group was significantly higher than that in normal and high BMI groups, the abundances of Firmicutes in the low and normal groups were significantly lower than that in high BMI groups. At the genus level, the abundance of Haemophilus in the low group was significantly higher than that in high BMI group, and the abundances of Streptococcus in the low and normal BMI groups were significantly lower than that in the high BMI group. Conclusions 1. The sputum microbiota of AECOPD patients in different BMI groups covered almost all microbiota, and BMI had no significant association with total number of respiratory tract microbiota or α-diversity in AECOPD patients. However, there was a significant difference in the PCoA between different BMI groups. 2. The microbiota structure of AECOPD patients differed in different BMI groups. Gram-negative bacteria (G-) in the respiratory tract of patients predominated in the low BMI group, while gram-positive bacteria (G+) predominated in the high BMI group.
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Affiliation(s)
- Yang Cao
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaolin Chen
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Shu
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Shi
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mingjing Wu
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xueli Wang
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kaili Deng
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Wei
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiaxin Yan
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ganzhu Feng
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Huang Z, Gao J, Peng C, Song J, Xie Z, Jia J, Li H, Zhao S, Liang Y, Gong B. The Effect of the Microalgae Chlorella vulgaris on the Gut Microbiota of Juvenile Nile Tilapia ( Oreochromis niloticus) Is Feeding-Time Dependent. Microorganisms 2023; 11:microorganisms11041002. [PMID: 37110425 PMCID: PMC10146053 DOI: 10.3390/microorganisms11041002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Chlorella vulgaris is one of the most commonly used microalgae in aquaculture feeds. It contains high concentrations of various kinds of nutritional elements that are involved in the physiological regulation of aquaculture animals. However, few studies have been conducted to illustrate their influence on the gut microbiota in fish. In this work, the gut microbiota of Nile tilapia (Oreochromis niloticus) (average weight is 6.64 g) was analyzed by high-throughput sequencing of the 16S rRNA gene after feeding with 0.5% and 2% C. vulgaris additives in diets for 15 and 30 days (average water temperature was 26 °C). We found that the impact of C. vulgaris on the gut microbiota of Nile tilapia was feeding-time dependent. Only by feeding for 30 days (not 15 days) did the addition of 2% C. vulgaris to diets significantly elevate the alpha diversity (Chao1, Faith pd, Shannon, Simpson, and the number of observed species) of the gut microbiota. Similarly, C. vulgaris exerted a significant effect on the beta diversity (Bray-Curtis similarity) of the gut microbiota after feeding for 30 days (not 15 days). During the 15-day feeding trial, LEfSe analysis showed that Paracoccus, Thiobacillus, Dechloromonas, and Desulfococcus were enriched under 2% C. vulgaris treatment. During the 30-day feeding trial, Afipia, Ochrobactrum, Polymorphum, Albidovulum, Pseudacidovorax, and Thiolamprovum were more abundant in 2% C. vulgaris-treated fish. C. vulgaris promoted the interaction of gut microbiota in juvenile Nile tilapia by increasing the abundance of Reyranella. Moreover, during the feeding time of 15 days, the gut microbes interacted more closely than those during the feeding time of 30 days. This work will be valuable for understanding how C. vulgaris in diets impacts the gut microbiota in fish.
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Affiliation(s)
- Zhicheng Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinyan Gao
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Chunyan Peng
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Jingjing Song
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Zongsheng Xie
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Jixin Jia
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Haochen Li
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Gong
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
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Yang P, Wu W, Chen J, Jiang S, Zheng Z, Deng Y, Lu J, Wang H, Zhou Y, Geng Y, Wang K. Thermotolerance improvement of engineered Saccharomyces cerevisiae ERG5 Delta ERG4 Delta ERG3 Delta, molecular mechanism, and its application in corn ethanol production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:66. [PMID: 37046321 PMCID: PMC10091661 DOI: 10.1186/s13068-023-02312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND The thermotolerant yeast is beneficial in terms of efficiency improvement of processes and reduction of costs, while Saccharomyces cerevisiae does not efficiently grow and ferment at high-temperature conditions. The sterol composition alteration from ergosterol to fecosterol in the cell membrane of S. cerevisiae affects the thermotolerant capability. RESULTS In this study, S. cerevisiae ERG5, ERG4, and ERG3 were knocked out using the CRISPR-Cas9 approach to impact the gene expression involved in ergosterol synthesis. The highest thermotolerant strain was S. cerevisiae ERG5ΔERG4ΔERG3Δ, which produced 22.1 g/L ethanol at 37 °C using the initial glucose concentration of 50 g/L with an increase by 9.4% compared with the wild type (20.2 g/L). The ethanol concentration of 9.4 g/L was produced at 42 ℃, which was 2.85-fold of the wild-type strain (3.3 g/L). The molecular mechanism of engineered S. cerevisiae at the RNA level was analyzed using the transcriptomics method. The simultaneous deletion of S. cerevisiae ERG5, ERG4, and ERG3 caused 278 up-regulated genes and 1892 down-regulated genes in comparison with the wild-type strain. KEGG pathway analysis indicated that the up-regulated genes relevant to ergosterol metabolism were ERG1, ERG11, and ERG5, while the down-regulated genes were ERG9 and ERG26. S. cerevisiae ERG5ΔERG4ΔERG3Δ produced 41.6 g/L of ethanol at 37 °C with 107.7 g/L of corn liquefied glucose as carbon source. CONCLUSION Simultaneous deletion of ERG5, ERG4, and ERG3 resulted in the thermotolerance improvement of S. cerevisiae ERG5ΔERG4ΔERG3Δ with cell viability improvement by 1.19-fold at 42 °C via modification of steroid metabolic pathway. S. cerevisiae ERG5ΔERG4ΔERG3Δ could effectively produce ethanol at 37 °C using corn liquefied glucose as carbon source. Therefore, S. cerevisiae ERG5ΔERG4ΔERG3Δ had potential in ethanol production at a large scale under supra-optimal temperature.
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Affiliation(s)
- Peizhou Yang
- School of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China.
| | - Wenjing Wu
- School of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Jianchao Chen
- School of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Suwei Jiang
- Department of Biological, Food and Environment Engineering, Hefei University, 158 Jinxiu Avenue, Hefei, 230601, China
| | - Zhi Zheng
- School of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Yanhong Deng
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Jiuling Lu
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Hu Wang
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Yong Zhou
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Yuyou Geng
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Kanglin Wang
- Hefei Knature Bio-Pharm Co., Ltd., Hefei, 231131, China
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Naik T, Sharda M, C P L, Virbhadra K, Pandit A. High-quality single amplicon sequencing method for illumina MiSeq platform using pool of 'N' (0-10) spacer-linked target specific primers without PhiX spike-in. BMC Genomics 2023; 24:141. [PMID: 36959538 PMCID: PMC10037784 DOI: 10.1186/s12864-023-09233-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/07/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Illumina sequencing platform requires base diversity in the initial 11 cycles for efficient cluster identification and colour matrix estimation. This limitation yields low-quality data for amplicon libraries having homogeneous base composition. Spike-in of PhiX library ensures base diversity but reduces the overall number of sequencing reads for data analysis. To overcome such low diversity issues during amplicon sequencing on illumina platforms, we developed a high throughput single amplicon sequencing method by introducing 'N' (0-10) spacers in target gene amplification primers that are pooled for simple handling. RESULT We evaluated the efficiency of 'N' (0-10) spacer-linked primers by targeting bacterial 16S V3-V4 region, demonstrating heterogeneous base library construction. The addition of 'N' (0-10) spacers causes sequencing frameshift at every base that leads to base diversity and produces heterogeneous high quality reads within a single amplicon library. We have written a python based command-line software,"MetReTrim", to trim the 'N' (0-10) spacers from the raw reads ( https://github.com/Mohak91/MetReTrim ). We further demonstrated the accuracy of this method by comparative mock community analysis with standard illumina V3-V4 primer method. The ZymoBIOMICS™ microbial community DNA standard was used as a control for this study. We performed data analysisusing the DADA2 pipeline where taxonomy was assigned using SILVA database as reference. We observed no difference between the communities represented by our method and standard illumina V3-V4 primer method. CONCLUSION This method eliminates the need for PhiX spike-in for single amplicon sequencing on illumina MiSeq platform. This allows for sequencing of more number of samples in a run and a reduction in the overall cost. Given that Illumina sequencing works on SBS chemistry irrespective of the platform (such as HiSeq, MiSeq, NextSeq, NovaSeq, etc.) we propose that this strategy of using 'N' (0-10) spacer-linked primer design can be adopted for generating high-quality single locus amplicon sequencing in a high throughput manner across the illumina platform subject to further validation.
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Affiliation(s)
- Tejali Naik
- National Centre for Biological Science, Tata Institute of Fundamental Research, Bengaluru, Karnataka, 560065, India
| | - Mohak Sharda
- National Centre for Biological Science, Tata Institute of Fundamental Research, Bengaluru, Karnataka, 560065, India
- School of Life Science, The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bengaluru, Karnataka, 560064, India
| | - Lakshminarayanan C P
- National Centre for Biological Science, Tata Institute of Fundamental Research, Bengaluru, Karnataka, 560065, India
| | - Kumar Virbhadra
- National Centre for Biological Science, Tata Institute of Fundamental Research, Bengaluru, Karnataka, 560065, India
| | - Awadhesh Pandit
- National Centre for Biological Science, Tata Institute of Fundamental Research, Bengaluru, Karnataka, 560065, India.
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Chattopadhyay S, Ramachandran P, Malayil L, Mongodin EF, Sapkota AR. Conventional tobacco products harbor unique and heterogenous microbiomes. ENVIRONMENTAL RESEARCH 2023; 220:115205. [PMID: 36592812 PMCID: PMC9898174 DOI: 10.1016/j.envres.2022.115205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 12/08/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
While an increasing number of studies have evaluated tobacco microbiomes, comparative microbiome analyses across diverse tobacco products are non-existent. Moreover, to our knowledge, no previous studies have characterized the metabolically-active (live) fraction of tobacco bacterial communities and compared them across products. To address these knowledge gaps, we compared bacterial communities across four commercial products (cigarettes, little cigars, cigarillos and hookah) and one research cigarette product. After total DNA extraction (n = 414) from all samples, the V3V4 region of the 16S rRNA gene was sequenced on the Illumina HiSeq platform. To identify metabolically-active bacterial communities within these products, we applied a coupled 5-bromo-2'-deoxyuridine labeling and sequencing approach to a subset of samples (n = 56). Each tobacco product was characterized by its signature microbiome, along with a shared microbiome across all tobacco products consisting of Pseudomonas aeruginosa, P. putida, P. alcaligenes, Bacillus subtilis, and Klebsiella pneumoniae. Comparing across products (using Linear discriminant analysis Effect Size (LEfSe)), a significantly higher (p < 0.05) relative abundance of Klebsiella and Acinetobacter was observed in commercial cigarettes, while a higher relative abundance of Pseudomonas and Pantoea was observed in research cigarettes. Methylorubrum and Paenibacillus were higher in hookah, and Brevibacillus, Lactobacillus, Bacillus, Lysinibacillus, and Staphylococcus were higher in little cigars and cigarillos. Across all products, the majority of the metabolically-active bacterial communities belonged to the genus Pseudomonas, followed by several genera within the Firmicutes phylum (Bacillus, Terribacillus, and Oceanobacillus). Identification of some metabolically-active pathogens such as Bacillus cereus and Haemophilus parainfluenzae in commercial products is of concern because of the potential for these microorganisms to be transferred to users' respiratory tracts via mainstream smoke. Future work is warranted to evaluate the potential impact of these tobacco bacterial communities on users' oral and lung microbiomes, which play such an important role on the spectrum from health to disease.
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Affiliation(s)
- Suhana Chattopadhyay
- Maryland Institute of Applied Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Padmini Ramachandran
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, College Park, MD, USA
| | - Leena Malayil
- Maryland Institute of Applied Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amy R Sapkota
- Maryland Institute of Applied Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA.
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21
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Dieng CC, Ford CT, Lerch A, Doniou D, Vegesna K, Janies D, Cui L, Amoah L, Afrane Y, Lo E. Genetic variations of Plasmodium falciparum circumsporozoite protein and the impact on interactions with human immunoproteins and malaria vaccine efficacy. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105418. [PMID: 36841398 DOI: 10.1016/j.meegid.2023.105418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
In October 2021, the world's first malaria vaccine RTS,S was endorsed by WHO for broad use in children, despite its low efficacy. This study examined polyclonal infections and the associations of parasite genetic variations with binding affinity to human leukocyte antigen (HLA). Multiplicity of infection was determined by amplicon deep sequencing of PfMSP1. Genetic variations in PfCSP were examined across 88 samples from Ghana and analyzed together with 1655 PfCSP sequences from other African and non-African isolates. Binding interactions of PfCSP peptide variants and HLA were predicted using NetChop and HADDOCK. High polyclonality was detected among infections, with each infection harboring multiple non-3D7 PfCSP variants. Twenty-seven PfCSP haplotypes were detected in the Ghanaian samples, and they broadly represented PfCSP diversity across Africa. The number of genetic differences between 3D7 and non-3D7 PfCSP variants does not influence binding to HLA. However, CSP peptide length after proteolytic degradation significantly affects its molecular weight and binding affinity to HLA. Despite the high diversity of HLA, the majority of the HLAI and II alleles interacted/bound with all Ghana CSP peptides. Multiple non-3D7 strains among P. falciparum infections could impact the effectiveness of RTS,S. Longer peptides of the Th2R/Th3R CSP regions should be considered in future versions of RTS,S.
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Affiliation(s)
- Cheikh Cambel Dieng
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Colby T Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Anita Lerch
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Dickson Doniou
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kovidh Vegesna
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Linda Amoah
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana; West Africa Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Yaw Afrane
- Department of Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, USA.
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Influence of Hormonal Contraceptive Use and HIV on Cervicovaginal Cytokines and Microbiota in Malawi. mSphere 2023; 8:e0058522. [PMID: 36622252 PMCID: PMC9942570 DOI: 10.1128/msphere.00585-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Important questions remain on how hormonal contraceptives alter the local immune environment and the microbiota in the female genital tract and how such effects may impact susceptibility to HIV infection. We leveraged samples from a previously conducted clinical trial of Malawian women with (n = 73) and without (n = 24) HIV infection randomized to depot medroxyprogesterone acetate (DMPA) or the levonogestrel implant in equal numbers within each group and determined the effects of these hormonal contraceptives (HCs) on the vaginal immune milieu and the composition of the vaginal microbiota. Longitudinal data for soluble immune mediators, measured by multiplex bead arrays and enzyme-linked immunosorbent assays (ELISAs), and vaginal microbiota, assessed by 16S rRNA gene amplicon, were collected prior to and over a period of 180 days post-HC initiation. DMPA and levonogestrel had only minimal effects on the vaginal immune milieu and microbiota. In women with HIV, with the caveat of a small sample size, there was an association between the median log10 change in the interleukin-12 (IL-12)/IL-10 ratio in vaginal fluid at day 180 post-HC compared to baseline when these women were classified as having a community state type (CST) IV vaginal microbiota and were randomized to DMPA. Long-lasting alterations in soluble immune markers or shifts in microbiota composition were not observed. Furthermore, women with HIV did not exhibit increased viral shedding in the genital tract after HC initiation. Consistent with the results of the ECHO (Evidence for Contraceptive Options and HIV Outcomes) trial, our data imply that the progestin-based HC DMPA and levonorgestrel are associated with minimal risk for women with HIV. (This study has been registered at ClinicalTrials.gov under registration no. NCT02103660). IMPORTANCE The results of the Evidence for Contraceptive Options and HIV Outcomes (ECHO) trial, the first large randomized controlled clinical trial comparing the HIV acquisition risk of women receiving DMPA, the levonorgestrel (LNG) implant, or the copper intrauterine device (IUD), did not reveal an increased risk of HIV acquisition for women on any of these three contraceptives. Our study results confirm that the two different progestin-based hormonal contraceptives DMPA and levonogestrel will not increase the risk for HIV infection. Furthermore, DMPA and levonogestrel have only minimal effects on the immune milieu and the microbiota in the vaginal tract, attesting to the safety of these hormonal contraceptives.
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Dixon M, Dunlop AL, Corwin EJ, Kramer MR. Joint effects of individual socioeconomic status and residential neighborhood context on vaginal microbiome composition. Front Public Health 2023; 11:1029741. [PMID: 36761121 PMCID: PMC9902942 DOI: 10.3389/fpubh.2023.1029741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction The vaginal microbiome is a dynamic ecosystem that is important for women's health. Its composition has been associated with risk for menopausal symptoms, sexually transmitted infections, gynecologic cancer, and preterm birth. Conventional risk factors for a vaginal microbiome linked with these adverse health outcomes include sexual behaviors, hygiene practices, individual social factors, and stress levels. However, there has been limited research on socio-contextual determinants, and whether neighborhood context modifies the association with individual socioeconomic factors. Methods Socioeconomically diverse pregnant African American women in Atlanta, Georgia (n = 439) provided residential addresses and first trimester vaginal swab samples, which underwent sequencing, taxonomic classification, and assignment into mutually exclusive CST (community state types) via hierarchical clustering. Linear probability models were used to estimate prevalence differences (PD) for the associations of neighborhood factors with vaginal microbiome CST and to evaluate for additive interaction with maternal level of education, health insurance type, and recruitment hospital. Results Factors such as higher (vs. lower) maternal education, private (vs. public) insurance, and private (vs. public) hospital were associated with higher prevalence of Lactobacillus-dominant vaginal microbiome CSTs typically associated with better health outcomes. When considering the joint effects of these individual socioeconomic status and residential neighborhood factors on vaginal microbiome CST, most combinations showed a greater than additive effect among the doubly exposed; however, in the case of local income homogeneity and local racial homogeneity, there was evidence of a crossover effect between those with less-advantaged individual socioeconomic status and those with more-advantaged individual socioeconomic status. Compared to women at the public hospital who lived in economically diverse neighborhoods, women at the private hospital who lived in economically diverse neighborhoods had a 21.9% higher prevalence of Lactobacillus-dominant CSTs, while women at the private hospital who lived in less economically diverse neighborhoods (the doubly exposed) had only an 11.7% higher prevalence of Lactobacillus-dominant CSTs, showing a crossover effect (interaction term p-value = 0.004). Discussion In this study, aspects of residential neighborhood context were experienced differently by women on the basis of their individual resources, and the joint effects of these exposures on vaginal microbiome CST showed a departure from simple additivity for some factors.
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Affiliation(s)
- Meredith Dixon
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Anne L. Dunlop
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States,Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | | | - Michael R. Kramer
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States,*Correspondence: Michael R. Kramer ✉
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Xiong ZR, Sogin JH, Worobo RW. Microbiome analysis of raw honey reveals important factors influencing the bacterial and fungal communities. Front Microbiol 2023; 13:1099522. [PMID: 36713191 PMCID: PMC9877413 DOI: 10.3389/fmicb.2022.1099522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Raw honeys contain diverse microbial communities. Previous studies have focused on isolating bacteria and fungi that are culturable, while missing a large proportion of the microbial community due to culture-based constraints. This study utilized next-generation sequencing (NGS) to analyze the composition of microorganisms in raw honey; these data can reveal environmental and physicochemical variables that are associated with different microbial communities. To examine the microbial composition (bacteria and fungi) of raw honey and analyze its association with physicochemical properties, four types of honey (monofloral, wildflower, manuka, and feral; n total = 36) were analyzed via amplicon metagenomics. The analyzed honey samples had relatively similar bacterial communities but more distinct and diverse fungal communities. Honey type was determined as a significant factor influencing alpha and beta diversity metrics of bacterial and fungal communities. For the bacterial communities, titratable acidity (TA) was associated with community richness and diversity. For the fungal communities, Brix, TA, and color were associated with community richness, while water activity and color were associated with community diversity. Additionally, important bacterial and fungal amplicon sequence variants (ASVs) that influenced the overall community were identified. Results from this study provide important insights into the microbial communities associated with different types of raw honey, which could improve our understanding of microbial dynamics in beehives, improve honey production, and prevent honeybee disease.
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Affiliation(s)
- Zirui Ray Xiong
- Department of Food Science, Cornell University, Ithaca, NY, United States
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Tuddenham S, Gajer P, Burke AE, Murphy C, Klein SL, Stennett CA, Wilgus B, Ravel J, Ghanem KG, Brotman RM. Lactobacillus-dominance and rapid stabilization of vaginal microbiota in combined oral contraceptive pill users examined through a longitudinal cohort study with frequent vaginal sampling over two years. EBioMedicine 2023; 87:104407. [PMID: 36529102 PMCID: PMC9792759 DOI: 10.1016/j.ebiom.2022.104407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV), a condition in which vaginal Lactobacillus spp. are in low abundance, is associated with vulvovaginal symptoms, obstetric outcomes and urogenital infections. Recurrent BV is difficult to manage, and emerging data indicate a reduced risk of BV with the use of hormonal contraception (HC). Despite widespread use, little longitudinal data is available on whether, and in what timeframe, combined oral contraceptive pills (COCs) may act to affect vaginal microbiota stability and Lactobacillus dominance. METHODS We compared the vaginal microbiota of reproductive-age cisgender women during intervals on combined estrogen and progestin COCs with non-use intervals in a 2-year observational study. Vaginal microbiota were characterized by 16S rRNA gene amplicon sequencing. FINDINGS COC users were more likely to have Lactobacillus-dominated microbiota and more stable microbiota over time. Stability increased and then plateaued four weeks after COC initiation. The associations between COCs and Lactobacillus spp. dominance, and microbiota stability, were statistically significant for White, but not African American women; however sample size was limited for African American participants. Findings were similar for other forms of HC and when excluding samples collected during menses. INTERPRETATION Our study provides a methodologic framework to evaluate observational longitudinal microbiota data with exposure crossovers. We found COCs are associated with vaginal microbiota stability and a Lactobacillus-dominated state. COCs appear to impact stability within a month of initiation. Our findings have clinical implications for how soon benefits can be expected in (at least White) patients initiating COCs, and support the need for larger prospective trials to verify our results in ethnically diverse populations. FUNDING R01-AI089878.
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Affiliation(s)
- Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anne E Burke
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Catherine Murphy
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christina A Stennett
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Barbara Wilgus
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Khalil G Ghanem
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
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26
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Liptáková A, Čurová K, Záhumenský J, Visnyaiová K, Varga I. Microbiota of female genital tract – functional overview of microbial flora from vagina to uterine tubes and placenta. Physiol Res 2022. [DOI: 10.33549/physiolres.934960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Microorganisms and eukaryotic human cells coexist in synergistic relationships in nearly every niche of the human body. The female genital tract consisting of the vagina, uterus with its cervix and endometrium, uterine tubes and ovaries – harbors its own typical microbiota, which accounts for 9 % of the total bacterial population in females. To this organ system, we also assigned the microbiome of the placenta, which has not been studied much until now. Among the spectrum of microbial species, the female genital tract is mainly dominated by Lactobacillus species, which are considered to be one of the simplest yet most important microbial communities. However, this relationship between macro- and micro-organisms seems to have a number of physiological functions, e.g., the vaginal and cervical microbiota have unique impact on reproductive health. The aim of this review was to provide current view on female genital tract microbiota and its role in reproductive health. We describe in detail the association of vaginal or tubal epithelium with microbiota or the role of microbiota in normal placental function.
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Affiliation(s)
| | - K Čurová
- Department of Medical and Clinical Microbiology, Faculty of Medicine, University of P. J. Šafárik, Košice, Slovak Republic.
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27
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LIPTÁKOVÁ A, ČUROVÁ K, ZÁHUMENSKÝ J, VISNYAIOVÁ K, VARGA I. Microbiota of female genital tract - functional overview of microbial flora from vagina to uterine tubes and placenta. Physiol Res 2022; 71:S21-S33. [PMID: 36592438 PMCID: PMC9853993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microorganisms and eukaryotic human cells coexist in synergistic relationships in nearly every niche of the human body. The female genital tract consisting of the vagina, uterus with its cervix and endometrium, uterine tubes and ovaries - harbors its own typical microbiota, which accounts for 9 % of the total bacterial population in females. To this organ system, we also assigned the microbiome of the placenta, which has not been studied much until now. Among the spectrum of microbial species, the female genital tract is mainly dominated by Lactobacillus species, which are considered to be one of the simplest yet most important microbial communities. However, this relationship between macro- and micro-organisms seems to have a number of physiological functions, e.g., the vaginal and cervical microbiota have unique impact on reproductive health. The aim of this review was to provide current view on female genital tract microbiota and its role in reproductive health. We describe in detail the association of vaginal or tubal epithelium with microbiota or the role of microbiota in normal placental function.
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Affiliation(s)
- Adriana LIPTÁKOVÁ
- Institute of Microbiology, Faculty of Medicine, Comenius University in Bratislava, Slovak Republic
| | - Katarína ČUROVÁ
- Department of Medical and Clinical Microbiology, Faculty of Medicine, University of P. J. Šafárik in Košice, Slovak Republic
| | - Jozef ZÁHUMENSKÝ
- Department of Gynecology and Obstetrics, Faculty of Medicine, Comenius University in Bratislava and University Hospital Bratislava, Slovak Republic
| | - Kristína VISNYAIOVÁ
- Department of Gynecology and Obstetrics, Faculty of Medicine, Comenius University in Bratislava and University Hospital Bratislava, Slovak Republic
| | - Ivan VARGA
- Institute of Histology and Embryology, Faculty of Medicine, Comenius University in Bratislava, Slovak Republic
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28
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Malayil L, Ramachandran P, Chattopadhyay S, Allard SM, Bui A, Butron J, Callahan MT, Craddock HA, Murray R, East C, Sharma M, Kniel K, Micallef S, Hashem F, Gerba CP, Ravishankar S, Parveen S, May E, Handy E, Kulkarni P, Anderson-Coughlin B, Craighead S, Gartley S, Vanore A, Duncan R, Foust D, Haymaker J, Betancourt W, Zhu L, Mongodin EF, Sapkota A, Pop M, Sapkota AR. Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15019-15033. [PMID: 36194536 PMCID: PMC9632240 DOI: 10.1021/acs.est.2c02281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.
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Affiliation(s)
- Leena Malayil
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Padmini Ramachandran
- Office
of Regulatory Science, Division of Microbiology, United States Food and Drug Administration, HFS-712, 5001 Campus Drive, College Park, Maryland 20740, United States
| | - Suhana Chattopadhyay
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Sarah M. Allard
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Anthony Bui
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Jicell Butron
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mary Theresa Callahan
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Hillary A. Craddock
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Rianna Murray
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Cheryl East
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Manan Sharma
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Kalmia Kniel
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shirley Micallef
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Fawzy Hashem
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Charles P. Gerba
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Sadhana Ravishankar
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Salina Parveen
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric May
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric Handy
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Prachi Kulkarni
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Brienna Anderson-Coughlin
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shani Craighead
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Samantha Gartley
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Adam Vanore
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Rico Duncan
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Derek Foust
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Joseph Haymaker
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Walter Betancourt
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Libin Zhu
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Emmanuel F. Mongodin
- Institute
for Genome Sciences, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Amir Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mihai Pop
- Department
of Computer Science and Center for Bioinformatics and Computational
Biology, University of Maryland, College Park, Maryland 20742, United States
| | - Amy R. Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
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29
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Ndungo E, Holm JB, Gama S, Buchwald AG, Tennant SM, Laufer MK, Pasetti MF, Rasko DA. Dynamics of the Gut Microbiome in Shigella-Infected Children during the First Two Years of Life. mSystems 2022; 7:e0044222. [PMID: 36121169 PMCID: PMC9600951 DOI: 10.1128/msystems.00442-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 02/02/2023] Open
Abstract
Shigella continues to be a major contributor to diarrheal illness and dysentery in children younger than 5 years of age in low- and middle-income countries. Strategies for the prevention of shigellosis have focused on enhancing adaptive immunity. The interaction between Shigella and intrinsic host factors, such as the microbiome, remains unknown. We hypothesized that Shigella infection would impact the developing microbial community in infancy and, conversely, that changes in the gastrointestinal microbiome may predispose infections. To test this hypothesis, we characterized the gastrointestinal microbiota in a longitudinal birth cohort from Malawi that was monitored for Shigella infection using 16S rRNA amplicon sequencing. Children with at least one Shigella quantitative polymerase chain reaction (qPCR) positive sample during the first 2 years of life (cases) were compared to uninfected controls that were matched for sex and age. Overall, the microbial species diversity, as measured by the Shannon diversity index, increased over time, regardless of case status. At early time points, the microbial community was dominated by Bifidobacterium longum and Escherichia/Shigella. A greater abundance of Prevotella 9 and Bifidobacterium kashiwanohense was observed at 2 years of age. While no single species was associated with susceptibility to Shigella infection, significant increases in Lachnospiraceae NK4A136 and Fusicatenibacter saccharivorans were observed following Shigella infection. Both taxa are in the family Lachnospiraceae, which are known short-chain fatty acid producers that may improve gut health. Our findings identified temporal changes in the gastrointestinal microbiota associated with Shigella infection in Malawian children and highlight the need to further elucidate the microbial communities associated with disease susceptibility and resolution. IMPORTANCE Shigella causes more than 180 million cases of diarrhea globally, mostly in children living in poor regions. Infection can lead to severe health impairments that reduce quality of life. There is increasing evidence that disruptions in the gut microbiome early in life can influence susceptibility to illnesses. A delayed or impaired reconstitution of the microbiota following infection can further impact overall health. Aiming to improve our understanding of the interaction between Shigella and the developing infant microbiome, we investigated changes in the gut microbiome of Shigella-infected and uninfected children over the course of their first 2 years of life. We identified species that may be involved in recovery from Shigella infection and in driving the microbiota back to homeostasis. These findings support future studies into the elucidation of the interaction between the microbiota and enteric pathogens in young children and into the identification of potential targets for prevention or treatment.
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Affiliation(s)
- Esther Ndungo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Johanna B. Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Syze Gama
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Andrea G. Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sharon M. Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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30
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France MT, Brown SE, Rompalo AM, Brotman RM, Ravel J. Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics. PLoS One 2022; 17:e0275908. [PMID: 36288274 PMCID: PMC9604009 DOI: 10.1371/journal.pone.0275908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
It has been suggested that the human microbiome might be vertically transmitted from mother to offspring and that early colonizers may play a critical role in development of the immune system. Studies have shown limited support for the vertical transmission of the intestinal microbiota but the derivation of the vaginal microbiota remains largely unknown. Although the vaginal microbiota of children and reproductive age women differ in composition, the vaginal microbiota could be vertically transmitted. To determine whether there was any support for this hypothesis, we examined the vaginal microbiota of daughter-mother pairs from the Baltimore metropolitan area (ages 14-27, 32-51; n = 39). We assessed whether the daughter's microbiota was similar in composition to their mother's using metataxonomics. Permutation tests revealed that while some pairs did have similar vaginal microbiota, the degree of similarity did not exceed that expected by chance. Genome-resolved metagenomics was used to identify shared bacterial strains in a subset of the families (n = 22). We found a small number of bacterial strains that were shared between mother-daughter pairs but identified more shared strains between individuals from different families, indicating that vaginal bacteria may display biogeographic patterns. Earlier-in-life studies are needed to demonstrate vertical transmission of the vaginal microbiota.
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Affiliation(s)
- Michael T. France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah E. Brown
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Anne M. Rompalo
- Division of Infectious Diseases, John Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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31
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Ahmad AA, Zhang J, Liang Z, Du M, Yang Y, Zheng J, Yan P, Long R, Tong B, Han J, Ding X. Age-dependent variations in rumen bacterial community of Mongolian cattle from weaning to adulthood. BMC Microbiol 2022; 22:213. [PMID: 36071396 PMCID: PMC9450343 DOI: 10.1186/s12866-022-02627-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that the rumen microbiome of Mongolian cattle has adapted to degrade the rough forage to provide sufficient energy to tolerate the harsh desert ecological conditions. However, little is known about the succession of rumen microbes in different developmental stages of post-weaning Mongolian cattle. METHODS Here, we examined the succession of the rumen microbial composition and structure of 15 post-weaning Mongolian cattle at three developmental stages i.e., 5 months (RM05), 18 months (RM18) and, 36 months (RM36) by using the 16S rRNA gene sequencing method. RESULTS We did not find any age-dependent variations in the ruminal concentrations of any volatile fatty acid (VFA) of Mongolian cattle. The diversity of the rumen bacterial community was significantly lower in RM05 group, which reached to stability with age. Bacteroidetes and Firmicutes were the two dominant phyla among all age groups. Phylum Actinobacteria was significantly higher in RM05 group, phyla Spirochaetes, and Tenericutes were highly abundant in RM18 group, and phyla Proteobacteria and Epsilonbacteraeota were enriched in RM36 group. Genera Prevotella_1, Bacteroides, and Bifidobacterium were abundant in RM05 group. The short chain fatty acid (SCFA) producing bacteria Rikenellaceae_RC9_gut_group showed high abundance in RM18 group and fiber degrading genus Alloprevotella was highly abundant in RM36 group. Random forest analysis identified Alloprevotella, Ileibacterium, and Helicobacter as important age discriminatory genera. In particular, the genera Ruminococcaceae_UCG-005, Bacteroides, Saccharofermentans, and Fibrobacter in RM05, genera [Eubacterium] coprostanoligenes_group, Erysipelotrichaceae_UCG-004, Helicobacter, Saccharofermentans, Papillibacter, and Turicibacter in RM18, and genera Rikenellaceae_RC9_gut_group, Lachnospiraceae_AC2044_group, and Papillibacter in RM36 showed the top interactions values in the intra-group interaction network. CONCLUSIONS The results showed that rumen microbiota of Mongolian cattle reached to stability and maturity with age after weaning. This study provides some theoretical evidence about the importance of functional specific rumen bacteria in different age groups. Further studies are needed to determine their actual roles and interactions with the host.
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Affiliation(s)
- Anum Ali Ahmad
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China.,State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jianbo Zhang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China.,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China
| | - Zeyi Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China
| | - Mei Du
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China
| | - Yayuan Yang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China
| | - Juanshan Zheng
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China
| | - RuiJun Long
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, The Research Center for Laboratory Animal Science, School of Life Sciences, Inner Mongolia University, Mongolia, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China. .,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China. .,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, 730050, China.
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32
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Yang P, Jiang S, Lu S, Jiang S, Jiang S, Deng Y, Lu J, Wang H, Zhou Y. Ethanol yield improvement in Saccharomyces cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta mutant and molecular mechanism exploration based on the metabolic flux and transcriptomics approaches. Microb Cell Fact 2022; 21:160. [PMID: 35964044 PMCID: PMC9375381 DOI: 10.1186/s12934-022-01885-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Saccharomyces cerevisiae generally consumes glucose to produce ethanol accompanied by the main by-products of glycerol, acetic acid, and lactic acid. The minimization of the formation of by-products in S. cerevisiae was an effective way to improve the economic viability of the bioethanol industry. In this study, S. cerevisiae GPD2, FPS1, ADH2, and DLD3 genes were knocked out by the Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR-Cas9) approach. The mechanism of gene deletion affecting ethanol metabolism was further elucidated based on metabolic flux and transcriptomics approaches. Results The engineered S. cerevisiae with gene deletion of GPD2, FPS1, ADH2, and DLD3 was constructed by the CRISPR-Cas9 approach. The ethanol content of engineered S. cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta increased by 18.58% with the decrease of glycerol, acetic acid, and lactic acid contents by 22.32, 8.87, and 16.82%, respectively. The metabolic flux analysis indicated that the carbon flux rethanol in engineered strain increased from 60.969 to 63.379. The sequencing-based RNA-Seq transcriptomics represented 472 differential expression genes (DEGs) were identified in engineered S. cerevisiae, in which 195 and 277 genes were significantly up-regulated and down-regulated, respectively. The enriched pathways of up-regulated genes were mainly involved in the energy metabolism of carbohydrates, while the down-regulated genes were mainly enriched in acid metabolic pathways. Conclusions The yield of ethanol in engineered S. cerevisiae increased with the decrease of the by-products including glycerol, acetic acid, and lactic acid. The deletion of genes GPD2, FPS1, ADH2, and DLD3 resulted in the redirection of carbon flux. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01885-3.
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Affiliation(s)
- Peizhou Yang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China.
| | - Shuying Jiang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Shuhua Lu
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Suwei Jiang
- Department of Biological, Food and Environment Engineering, Hefei University, 158 Jinxiu Avenue, Hefei, 230601, China
| | - Shaotong Jiang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Yanhong Deng
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Jiuling Lu
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Hu Wang
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Yong Zhou
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
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Bacterial communities of hookah tobacco products are diverse and differ across brands and flavors. Appl Microbiol Biotechnol 2022; 106:5785-5795. [PMID: 35927334 PMCID: PMC9361917 DOI: 10.1007/s00253-022-12079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022]
Abstract
Abstract Young adults are increasingly using non-cigarette products, such as hookahs, since they are perceived as healthier alternatives to cigarette smoking. However, hookah users are exposed to not only carcinogenic compounds but also microorganisms that may play an active role in the development of both infectious and chronic diseases among users. Nevertheless, existing hookah research in this area has focused only on microorganisms that may be transferred to users through the smoking apparatus and not on bacterial communities associated with hookah tobacco. To address this knowledge gap, we conducted time-series experiments on commercially available hookah brands (Al Fakher (flavors: two apple, mint, and watermelon) and Fumari (flavors: white gummy bear, ambrosia, and mint chocolate chill)) stored under three different temperature and relative humidity conditions over 14 days. To characterize bacterial communities, the total DNA was extracted on days 0, 5, 9, and 14, PCR-amplified for the V3V4 region of the bacterial 16S rRNA gene, sequenced on the Illumina HiSeq platform, and analyzed using R. Diversity (alpha and beta) analyses revealed that the microbiotas of Fumari and Al Fakher products differed significantly and that flavor had a significant effect on the hookah microbiota. Overall, Pseudomonas, Bacillus, Sphingomonas, and Methylobacterium were the predominant bacterial taxa across all products. Additionally, we observed compositional differences between hookah brands across the 14-day incubation. These data suggest that the bacterial communities of hookah tobacco are diverse and differ across brands and flavors, which may have critical implications regarding exposures to specific bacteria among hookah users. Key points • Commercial hookah products harbor diverse bacterial communities. • Brands and flavors impact the diversity of these communities. • Research on their viability and transmission to users’ respiratory tracts is needed. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12079-7.
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Mehta SD, Nandi D, Agingu W, Green SJ, Otieno FO, Bhaumik DK, Bailey RC. Longitudinal Changes in the Composition of the Penile Microbiome Are Associated With Circumcision Status, HIV and HSV-2 Status, Sexual Practices, and Female Partner Microbiome Composition. Front Cell Infect Microbiol 2022; 12:916437. [PMID: 35865819 PMCID: PMC9294230 DOI: 10.3389/fcimb.2022.916437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Penile microbiome composition has been associated with HSV-2 and HIV in men and with bacterial vaginosis (BV) and HSV-2 in female sex partners. This study sought to 1) characterize penile microbiome composition over a 1-year period and 2) identify factors associated with penile microbiome composition over time. Methods This prospective study of community-recruited heterosexual couples in Kenya measured penile and vaginal microbiomes via 16S ribosomal RNA gene amplicon sequencing at 4 time points over 1 year (1, 6, and 12 months after baseline). We used longitudinal mixed-effects modeling to assess associated demographic, behavioral, and disease factors and changes in community type, meatal taxa with the highest mean relative abundance, and alpha and beta diversity measures. We estimated group-based trajectories to elucidate compositional trends. Results Among 218 men with 740 observations, men had a median age of 26 years, 11.6% were living with HIV, and 46.1% were HSV-2 seropositive. We identified 7 penile community types that varied with circumcision status, female partner vaginal microbiome community state type (CST), condom use, and penile washing. Across varying analytic approaches, 50%-60% of men had stable penile microbiome compositions. Alpha diversity measures were lower for circumcised men and those who reported condom use; they were stable over time but higher if female partners had diverse CSTs or BV. BV was positively associated with the relative abundance of numerous individual penile taxa. The decreased Bray-Curtis similarity was more common for men with HSV-2, and HSV-2 was also associated with a lower relative abundance of Corynebacterium and Staphylococcus. Conclusions Over a 1-year period, penile microbiome composition was stable for a substantial proportion of men and was influenced by men's circumcision status, sexual practices, female partner's vaginal CST and BV status, and men's HSV-2 status. In the female genital tract, a diverse CST is often associated with poorer health outcomes. Our results contribute toward understanding whether this framework extends to the penile microbiome and whether diversity and the associated penile microbiome compositions influence susceptibility or resilience to poorer health outcomes in men. Focusing on understanding how these factors influence the penile microbiome may lead to therapeutic avenues for reduced HSV-2 and BV infections in men and their female sex partners.
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Affiliation(s)
- Supriya D. Mehta
- Department of Medicine, Division of Infectious Diseases, College of Medicine, Rush University, Chicago, IL, United States,Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois, Chicago, IL, United States,*Correspondence: Supriya D. Mehta,
| | - Debarghya Nandi
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois, Chicago, IL, United States
| | | | - Stefan J. Green
- Genomics and Microbiome Core Facility, College of Medicine, Rush University, Chicago, IL, United States
| | - Fredrick O. Otieno
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois, Chicago, IL, United States
| | - Dulal K. Bhaumik
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois, Chicago, IL, United States
| | - Robert C. Bailey
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois, Chicago, IL, United States
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Grant-Beurmann S, Jumare J, Ndembi N, Matthew O, Shutt A, Omoigberale A, Martin OA, Fraser CM, Charurat M. Dynamics of the infant gut microbiota in the first 18 months of life: the impact of maternal HIV infection and breastfeeding. MICROBIOME 2022; 10:61. [PMID: 35414043 PMCID: PMC9004197 DOI: 10.1186/s40168-022-01230-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Access to antiretroviral therapy (ART) during pregnancy and breastfeeding for mothers with HIV has resulted in fewer children acquiring HIV peri- and postnatally, resulting in an increase in the number of children who are exposed to the virus but are not infected (HEU). HEU infants have an increased likelihood of childhood infections and adverse growth outcomes, as well as increased mortality compared to their HIV-unexposed (HUU) peers. We explored potential differences in the gut microbiota in a cohort of 272 Nigerian infants born to HIV-positive and negative mothers in this study during the first 18 months of life. RESULTS The taxonomic composition of the maternal vaginal and gut microbiota showed no significant differences based on HIV status, and the composition of the infant gut microbiota at birth was similar between HUU and HEU. Longitudinal taxonomic composition of the infant gut microbiota and weight-for-age z-scores (WAZ) differed depending on access to breast milk. HEU infants displayed overall lower WAZ than HUU infants at all time points. We observed a significantly lower relative abundance of Bifidobacterium in HEU infants at 6 months postpartum. Breast milk composition also differed by time point and HIV infection status. The antiretroviral therapy drugs, lamivudine and nevirapine, as well as kynurenine, were significantly more abundant in the breast milk of mothers with HIV. Levels of tiglyl carnitine (C5) were significantly lower in the breast milk of mothers without HIV. ART drugs in the breast milk of mothers with HIV were associated with a lower relative abundance of Bifidobacterium longum. CONCLUSIONS Maternal HIV infection was associated with adverse growth outcomes of HEU infants in this study, and these differences persist from birth through at least 18 months, which is a critical window for the development of the immune and central nervous systems. We observed that the relative abundance of Bifidobacterium spp. was significantly lower in the gut microbiota of all HEU infants over the first 6 months postpartum, even if HEU infants were receiving breast milk. Breastfeeding was of benefit in our HEU infant cohort in the first weeks postpartum; however, ART drug metabolites in breast milk were associated with a lower abundance of Bifidobacterium. Video abstract.
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Affiliation(s)
- Silvia Grant-Beurmann
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jibreel Jumare
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Ashley Shutt
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Olivia A Martin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Claire M Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 2022; 31:2769-2795. [PMID: 35395127 DOI: 10.1111/mec.16460] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Thurman AR, Ravel J, Gajer P, Marzinke MA, Ouattara LA, Jacot T, Peet MM, Clark MR, Doncel GF. Vaginal Microbiota and Mucosal Pharmacokinetics of Tenofovir in Healthy Women Using a 90-Day Tenofovir/Levonorgestrel Vaginal Ring. Front Cell Infect Microbiol 2022; 12:799501. [PMID: 35350436 PMCID: PMC8957918 DOI: 10.3389/fcimb.2022.799501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/09/2022] [Indexed: 01/04/2023] Open
Abstract
Background A relationship between the vaginal microbiota and tenofovir (TFV) concentrations and activity after topical administration has been previously reported. Objective CONRAD A15-138 was a randomized, placebo-controlled Phase I study aimed at characterizing the safety, pharmacokinetics (PK), and pharmacodynamics (PD) of TFV and levonorgestrel (LNG) administered through a vaginal ring (IVR) for 90 days. Herein, we describe changes from baseline in the vaginal microbiota with IVR use and the impact of the vaginal microbiota on mucosal TFV PK. Methods The study screened 68 participants and randomized 47 (37 TFV/LNG, 10 placebo), assessing the vaginal microbiota by sequencing the V3–V4 regions of 16S rRNA genes prior to IVR insertion and monthly for 3 months. Concentrations of TFV in vaginal fluid (VF), and TFV and TFV-diphosphate (TFV-DP) in vaginal tissue, and modeled PD against HIV-1 in vitro were measured before and after treatment. Results There were no clinically significant changes in relative abundance of vaginal bacterial phylotypes from pre-insertion baseline at any month among active and placebo IVR users. There were no significant changes in community state type (CST) with IVR use. Participants with diverse, anaerobic CST IVA/B microbiota had higher in vivo release of TFV from the IVR compared to women with Lactobacillus-dominated (LbD) microbiota, who had expected in vivo TFV release rates. Median VF TFV concentrations were significantly higher among women with CST IVA/B microbiota in months 1 (3,135 ng/mg VF) and 2 (3,800 ng/mg). Women with LbD microbiota had significantly higher median VF TFV concentration (1,423 ng/mg) and median TFV (103 ng/mg) and TFV-DP (5,877 fmol/mg) tissue concentrations versus women with CST IVA/B microbiota at month 3. All women demonstrated a significant increase from pre-insertion baseline of in vitro HIV-1 inhibition by VF (p values <0.05). PD differences in tissue according to CST, however, were not statistically significant. Conclusion TFV/LNG IVR use did not change the vaginal microbiota nor increase the incidence of CST IVA/B. Vaginal microbiota, and in particular CST IVA/B, possibly through increased vaginal pH, impacted in vivo TFV release and cervicovaginal (CV) PK, but both PK and PD data suggest CV protection against HIV-1. Clinical Trial Registration ClinicalTrials.gov (#NCT03279120)
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Affiliation(s)
- Andrea R. Thurman
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
- *Correspondence: Andrea R. Thurman,
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Pawel Gajer
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mark A. Marzinke
- Departments of Pathology and Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Louise A. Ouattara
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Terry Jacot
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - M. Melissa Peet
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Meredith R. Clark
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Gustavo F. Doncel
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
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Deng W, Murugan S, Lindberg J, Chellappa V, Shen X, Pawitan Y, Vu TN. Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients. Front Genet 2022; 13:820493. [PMID: 35251131 PMCID: PMC8888970 DOI: 10.3389/fgene.2022.820493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 12/13/2022] Open
Abstract
Several fusion genes are directly involved in the initiation and progression of cancers. Numerous bioinformatics tools have been developed to detect fusion events, but they are mainly based on RNA-seq data. The whole-exome sequencing (WES) represents a powerful technology that is widely used for disease-related DNA variant detection. In this study, we build a novel analysis pipeline called Fuseq-WES to detect fusion genes at DNA level based on the WES data. The same method applies also for targeted panel sequencing data. We assess the method to real datasets of acute myeloid leukemia (AML) and prostate cancer patients. The result shows that two of the main AML fusion genes discovered in RNA-seq data, PML-RARA and CBFB-MYH11, are detected in the WES data in 36 and 63% of the available samples, respectively. For the targeted deep-sequencing of prostate cancer patients, detection of the TMPRSS2-ERG fusion, which is the most frequent chimeric alteration in prostate cancer, is 91% concordant with a manually curated procedure based on four other methods. In summary, the overall results indicate that it is challenging to detect fusion genes in WES data with a standard coverage of ∼ 15–30x, where fusion candidates discovered in the RNA-seq data are often not detected in the WES data and vice versa. A subsampling study of the prostate data suggests that a coverage of at least 75x is necessary to achieve high accuracy.
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Affiliation(s)
- Wenjiang Deng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sarath Murugan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xia Shen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Yudi Pawitan, ; Trung Nghia Vu,
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Yudi Pawitan, ; Trung Nghia Vu,
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Borgogna JLC, Anastario M, Firemoon P, Rink E, Ricker A, Ravel J, Brotman RM, Yeoman CJ. Vaginal microbiota of American Indian women and associations with measures of psychosocial stress. PLoS One 2021; 16:e0260813. [PMID: 34890405 PMCID: PMC8664215 DOI: 10.1371/journal.pone.0260813] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular-bacterial vaginosis (BV) is characterized by low levels of vaginal Lactobacillus species and is associated with higher risk of sexually transmitted infections (STI). Perceived psychosocial stress is associated with increased severity and persistence of infections, including STIs. American Indians have the highest rates of stress and high rates of STIs. The prevalence of molecular-BV among American Indian women is unknown. We sought to evaluate measures of psychosocial stress, such as historic loss (a multigenerational factor involving slavery, forced removal from one's land, legally ratified race-based segregation, and contemporary discrimination) and their association with the vaginal microbiota and specific metabolites associated with BV, in 70 Northwestern Plains American Indian women. Demographics, perceived psychosocial stressors, sexual practices, and known BV risk factors were assessed using a modified version of the American Indian Service Utilization, Psychiatric Epidemiology, Risk and Protective Factors Project survey. Self-collected mid-vaginal swabs were profiled for bacterial composition by 16S rRNA gene amplicon sequencing and metabolites quantified by targeted liquid-chromatography mass spectrometry. Sixty-six percent of the participants were classified as having molecular-BV, with the rest being either dominated by L. crispatus (10%) or L. iners (24%). High levels of lifetime trauma were associated with higher odds of having molecular-BV (adjusted Odds Ratio (aOR): 2.5, 95% Credible Interval (CrI): 1.1-5.3). Measures of psychosocial stress, including historic loss and historic loss associated symptoms, were significantly associated with lifestyle and behavioral practices. Higher scores of lifetime trauma were associated with increased concentrations of spermine (aFC: 3.3, 95% CrI: 1.2-9.2). Historic loss associated symptoms and biogenic amines were the major correlates of molecular-BV. Historical loss associated symptoms and lifetime trauma are potentially important underlying factors associated with BV.
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Affiliation(s)
- Joanna-Lynn C. Borgogna
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Michael Anastario
- Department of Health Promotion and Disease Prevention, Florida International University, Miami, Florida, United States of America
| | - Paula Firemoon
- Fort Peck Community College, Poplar, Montana, United States of America
| | - Elizabeth Rink
- Department of Health and Human Development, Montana State University, Bozeman, Montana, United States of America
| | - Adriann Ricker
- School of Public Health–Center for American Indian Health and School of Nursing, John Hopkins University, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Carl J. Yeoman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
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40
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Turpin R, Slopen N, Borgogna JLC, Yeoman CJ, He X, Miller RS, Klebanoff MA, Ravel J, Brotman RM. Perceived Stress and Molecular Bacterial Vaginosis in the National Institutes of Health Longitudinal Study of Vaginal Flora. Am J Epidemiol 2021; 190:2374-2383. [PMID: 34008013 DOI: 10.1093/aje/kwab147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Vaginal microbiota provide the first line of defense against urogenital infections primarily through protective actions of Lactobacillus species Perceived stress increases susceptibility to infection through several mechanisms, including suppression of immune function. We investigated whether stress was associated with deleterious changes to vaginal bacterial composition in a subsample of 572 women in the Longitudinal Study of Vaginal Flora, sampled from 1999 through 2002. Using Cox proportional hazards models, both unadjusted and adjusted for sociodemographic factors and sexual behaviors, we found that participants who exhibited a 5-unit-increase in Cohen's Perceived Stress Scale had greater risk (adjusted hazard ratio (HR) = 1.40, 95% confidence interval (CI): 1.13, 1.74) of developing molecular bacterial vaginosis (BV), a state with low Lactobacillus abundance and diverse anaerobic bacteria. A 5-unit increase in stress score was also associated with greater risks of transitioning from the L. iners-dominated community state type (26% higher) to molecular-BV (adjusted HR = 1.26, 95% CI: 1.01, 1.56) or maintaining molecular-BV from baseline (adjusted HR = 1.23, 95% CI: 1.01, 1.47). Inversely, women with baseline molecular-BV reporting a 5-unit stress increase were less likely to transition to microbiota dominated by L. crispatus, L. gasseri, or L. jensenii (adjusted HR = 0.81, 95% CI: 0.68, 0.99). These findings suggest that psychosocial stress is associated with vaginal microbiota composition, inviting a more mechanistic exploration of the relationship between psychosocial stress and molecular-BV.
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Jašarević E, Hill EM, Kane PJ, Rutt L, Gyles T, Folts L, Rock KD, Howard CD, Morrison KE, Ravel J, Bale TL. The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model. Nat Commun 2021; 12:6289. [PMID: 34725359 PMCID: PMC8560944 DOI: 10.1038/s41467-021-26634-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Newborns are colonized by maternal microbiota that is essential for offspring health and development. The composition of these pioneer communities exhibits individual differences, but the importance of this early-life heterogeneity to health outcomes is not understood. Here we validate a human microbiota-associated model in which fetal mice are cesarean delivered and gavaged with defined human vaginal microbial communities. This model replicates the inoculation that occurs during vaginal birth and reveals lasting effects on offspring metabolism, immunity, and the brain in a community-specific manner. This microbial effect is amplified by prior gestation in a maternal obesogenic or vaginal dysbiotic environment where placental and fetal ileum development are altered, and an augmented immune response increases rates of offspring mortality. Collectively, we describe a translationally relevant model to examine the defined role of specific human microbial communities on offspring health outcomes, and demonstrate that the prenatal environment dramatically shapes the postnatal response to inoculation.
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Affiliation(s)
- Eldin Jašarević
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Elizabeth M Hill
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Patrick J Kane
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay Rutt
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Trevonn Gyles
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lillian Folts
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kylie D Rock
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christopher D Howard
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kathleen E Morrison
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jacques Ravel
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Tracy L Bale
- Center for Epigenetic Research in Child Health and Brain Development, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA.
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Hou X, Zhang P, Du H, Chu W, Sun R, Qin S, Tian Y, Zhang Z, Xu F. Akkermansia Muciniphila Potentiates the Antitumor Efficacy of FOLFOX in Colon Cancer. Front Pharmacol 2021; 12:725583. [PMID: 34603035 PMCID: PMC8484791 DOI: 10.3389/fphar.2021.725583] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/24/2021] [Indexed: 12/24/2022] Open
Abstract
FOLFOX (oxaliplatin, fluorouracil and calcium folinate) is the first-line chemotherapy regimen for colon cancer therapy in the clinic. It provides superior efficacy than oxaliplatin alone, but the underlying mechanism remains unclear. In the present study, pharmacomicrobiomics integrated with metabolomics was conducted to uncover the role of the gut microbiome behind this. First, in vivo study demonstrated that FOLFOX exhibited better efficacy than oxaliplatin alone in colon cancer animal models. Second, 16S rDNA gene sequencing analysis showed that the abundance of Akkermansia muciniphila (A. muciniphila) remarkably increased in the FOLFOX treated individuals and positively correlated with the therapeutic effect. Third, further exploration confirmed A. muciniphila colonization significantly enhanced the anti-cancer efficacy of FOLFOX. Last, metabolomics analysis suggested dipeptides containing branched-chain amino acid (BCAA) might be responsible for gut bacteria mediated FOLFOX efficacy. In conclusion, our study revealed the key role of A. muciniphila in mediating FOLFOX efficacy, and manipulating A. muciniphila might serve as a novel strategy for colon cancer therapy.
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Affiliation(s)
- Xiaoying Hou
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Pei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Hongzhi Du
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Weihua Chu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Ruiqi Sun
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Siyuan Qin
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Zunjian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
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Wu H, Wu Z, Wang Y, Ding J, Zheng Y, Tang H, Yang L. Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old Overwintering Camellia sinensis. BIOLOGY 2021; 10:biology10100996. [PMID: 34681095 PMCID: PMC8533452 DOI: 10.3390/biology10100996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/23/2023]
Abstract
Simple Summary The freezing stress during overwintering brings great challenges to the normal growth of Camellia sinensis. The current research on C. sinensis mainly focuses on cold resistance, but less on freezing resistance. In the present study, the transcriptome and metabolome of C. sinensis under freezing stress were studied. Results showed that Pyr/PYL-PP2C-SnRK2 played a critical role in the signal transduction of freezing stress. Three metabolic pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis contributed to the freezing resistance of C. sinensis. This study provides substantial insights for the breeding of C. sinensis. Abstract Freezing stress in winter is the biggest obstacle to the survival of C. sinensis in mid-latitude and high-latitude areas, which has a great impact on the yield, quality, and even life of C. sinensis every year. In this study, transcriptome and metabolome were used to clarify the freezing resistance mechanism of 60-year-old natural overwintering C. sinensis under freezing stress. Next, 3880 DEGs and 353 DAMs were obtained. The enrichment analysis showed that pathways of MAPK and ABA played a key role in the signal transduction of freezing stress, and Pyr/PYL-PP2C-SnRK2 in the ABA pathway promoted stomatal closure. Then, the water holding capacity and the freezing resistance of C. sinensis were improved. The pathway analysis showed that DEGs and DAMs were significantly enriched and up-regulated in the three-related pathways of phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis. In addition, the carbohydrate and fatty acid synthesis pathways also had a significant enrichment, and the synthesis of these substances facilitated the freezing resistance. These results are of great significance to elucidate the freezing resistance mechanism and the freezing resistance breeding of C. sinensis.
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Mehta SD, Zulaika G, Otieno FO, Nyothach E, Agingu W, Bhaumik R, Green SJ, van Eijk AM, Kwaro D, Phillips-Howard PA. High Prevalence of Lactobacillus crispatus Dominated Vaginal Microbiome Among Kenyan Secondary School Girls: Negative Effects of Poor Quality Menstrual Hygiene Management and Sexual Activity. Front Cell Infect Microbiol 2021; 11:716537. [PMID: 34621690 PMCID: PMC8490761 DOI: 10.3389/fcimb.2021.716537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/30/2021] [Indexed: 01/05/2023] Open
Abstract
The vaginal microbiome (VMB) impacts numerous health outcomes, but evaluation among adolescents is limited. We characterized the VMB via 16S rRNA gene amplicon sequencing, and its association with Bacterial vaginosis (BV) and sexually transmitted infections (STIs; chlamydia, gonorrhea, trichomoniasis) among 436 schoolgirls in Kenya, median age 16.9 years. BV and STI prevalence was 11.2% and 9.9%, respectively, with 17.6% of girls having any reproductive tract infection. Three community state types (CST) accounted for 95% of observations: CST-I L.crispatus-dominant (N=178, BV 0%, STI 2.8%, sexually active 21%); CST-III L.iners-dominant (N=152, BV 3.3%, STI 9.7%, sexually active 35%); CST-IV G.vaginalis-dominant (N=83, BV 51.8%, STI 25.3%, sexually active 43%). In multivariable adjusted analyses, sexually active girls had increased odds of CST-III and CST-IV, and use of cloth to manage menses had 1.72-fold increased odds of CST-IV vs. CST-I. The predominance of L.crispatus-dominated VMB, substantially higher than observed in prior studies of young adult and adult women in sub-Saharan Africa, indicates that non-optimal VMB can be an acquired state. Interventions to maintain or re-constitute L.crispatus dominance should be considered even in adolescents.
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Affiliation(s)
- Supriya D. Mehta
- Division of Epidemiology & Biostatistics, University of Illinois at Chicago, Chicago, IL, United States,*Correspondence: Supriya D. Mehta,
| | - Garazi Zulaika
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Elizabeth Nyothach
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Runa Bhaumik
- Division of Epidemiology & Biostatistics, University of Illinois at Chicago, Chicago, IL, United States
| | - Stefan J. Green
- Department of Internal Medicine and Genomics and Microbiome Core Facility, Rush University, Chicago, IL, United States
| | - Anna Maria van Eijk
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Daniel Kwaro
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
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Tuddenham S, Stennett CA, Cone RA, Ravel J, Macintyre AN, Ghanem KG, He X, Brotman RM. Vaginal cytokine profile and microbiota before and after lubricant use compared with condomless vaginal sex: a preliminary observational study. BMC Infect Dis 2021; 21:973. [PMID: 34537015 PMCID: PMC8449901 DOI: 10.1186/s12879-021-06512-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/18/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Limited data suggest that personal lubricants may damage the vaginal mucosal epithelium, alter the vaginal microbiota, and increase inflammation. We compared vaginal cytokine profiles and microbiota before and after vaginal lubricant use and condomless vaginal sex. METHODS Reproductive-age women were recruited to a 10-week observational cohort study and were asked to self-collect vaginal samples and behavioral diaries daily. This nested case-control analysis utilized samples collected before and after self-reported condomless sexual activity with lubricants (22 case participants) and without lubricants (22 control participants). Controls were matched to cases on race/ethnicity. Microbiota composition was characterized by sequencing amplicons of the 16S rRNA gene V3-V4 regions. Cytokine concentrations were quantified using a magnetic bead 41-plex panel assay and read using a Bio-Plex 200 array reader. Wilcoxon signed-rank tests were used to assess baseline differences in vaginal cytokines between cases and controls as well as differences pre- and post-exposure. Linear mixed effects models were used to examine differences in relative post-to-pre change in each individual cytokine between matched cases and controls. Similar analyses were conducted for the microbiota data. RESULTS Mean age was 29.8 years (SD 6.8), and 63.6% were African American. There were few statistically significant changes in cytokines or microbiota before and after exposure in cases or controls. In mixed-effects modeling, the mean relative post-to-pre change of cytokines was higher in cases vs. controls for macrophage derived chemokine (MDC) (p = 0.03). The microbiota data revealed no significant changes when measured by similarity scores, diversity indexes and descriptive community state types (CST) transition analyses. However, post sexual activity, the mean relative abundance of L. crispatus decreased for those who used lubricants (particularly those who were L. iners-dominated prior to exposure). CONCLUSIONS Although there were overall few differences in the vaginal microbiota and cytokine profiles of lubricant users and controls before and after condomless vaginal sex, there was a trend toward decreases in relative abundance of L. crispatus following use of lubricant. Future larger studies that take into account osmolarity and composition of lubricants may provide additional insights.
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Affiliation(s)
- Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christina A Stennett
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Richard A Cone
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew N Macintyre
- Department of Medicine, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Khalil G Ghanem
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xin He
- School of Public Health, University of Maryland College Park, College Park, MD, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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Novak J, Ravel J, Ma B, Ferreira CST, Tristão ADR, Silva MG, Marconi C. Characteristics associated with Lactobacillus iners-dominated vaginal microbiota. Sex Transm Infect 2021; 98:353-359. [PMID: 34497114 DOI: 10.1136/sextrans-2020-054824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 08/29/2021] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE The protective role of Lactobacillus iners in the vaginal microbiota has been questioned. Recent studies have shown that L. iners is the dominating taxon in a large subset of women worldwide. The aim of this study was to identify sociodemographic, behavioural and clinical variables associated with L. iners-dominated community state type (CST) III in Brazilian women of reproductive age. PARTICIPANTS AND METHODS This study leveraged microbiota compositional data generated by sequencing of the V3-V4 16S rRNA gene from vaginal samples collected from 442 participants enrolled in a previous cross-sectional study that included 609 women in five geographical regions of Brazil. A total of 167 (27.4%) participants were excluded from the current study as they did not present a Lactobacillus-dominated vaginal microbiota. Data on sociodemographic and behavioural characteristics of the study population were obtained through face-to-face interviews. Participants were assigned to two study groups: those with L. iners-dominated CST III (n=222) and those with three distinct CSTs (I, II or V) dominated by another Lactobacillus spp. (n=220). Logistic regression analysis using a stepwise method was performed to test association between CST III and participants' characteristics, considering their OR and 95% CIs. RESULTS Among the population characteristics assessed, L. iners-dominated CST III was independently associated with having two or more sexual partners (OR 3.27; 95% CI 1.50 to 7.11) and microscopic detection of Candida sp. on vaginal smears (OR 2.24; 95% CI 1.02 to 4.89). Other characteristics were inversely associated with CST III, including condom use (OR 0.59; 95% CI 0.38 to 0.91), higher educational level (OR 0.61; 95% CI 0.41 to 0.91) and diet containing milk/dairy intake (OR 0.43; 95% CI 0.20 to 0.90). CONCLUSION Unprotected sex practices, number of sexual partners and lower educational levels may be useful for identifying women with L. iners-dominated microbiota and its suboptimal protective properties. L. iners microbiota does not seem to provide optimal protection against Candida sp. colonisation, warranting further investigation.
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Affiliation(s)
- Juliano Novak
- Department of Pathology, São Paulo State University (Unesp), Medical School, Botucatu, São Paulo, Brazil
| | - Jacques Ravel
- Department of Microbiology & Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Andrea da Rocha Tristão
- Department of Gynecology and Obstetrics, São Paulo State University (Unesp), Medical School, Botucatu, São Paulo, Brazil
| | - Marcia Guimaraes Silva
- Department of Pathology, São Paulo State University (Unesp), Medical School, Botucatu, São Paulo, Brazil
| | - Camila Marconi
- Department of Pathology, São Paulo State University (Unesp), Medical School, Botucatu, São Paulo, Brazil.,Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
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Merenstein D, Fraser CM, Roberts RF, Liu T, Grant-Beurmann S, Tan TP, Smith KH, Cronin T, Martin OA, Sanders ME, Lucan SC, Kane MA. Bifidobacterium animalis subsp. lactis BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome. Nutrients 2021; 13:nu13082814. [PMID: 34444974 PMCID: PMC8398419 DOI: 10.3390/nu13082814] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 01/04/2023] Open
Abstract
The administration of broad-spectrum antibiotics is often associated with antibiotic-associated diarrhea (AAD), and impacts gastrointestinal tract homeostasis, as evidenced by the following: (a) an overall reduction in both the numbers and diversity of the gut microbiota, and (b) decreased short-chain fatty acid (SCFA) production. Evidence in humans that probiotics may enhance the recovery of microbiota populations after antibiotic treatment is equivocal, and few studies have addressed if probiotics improve the recovery of microbial metabolic function. Our aim was to determine if Bifidobacterium animalis subsp. lactis BB-12 (BB-12)-containing yogurt could protect against antibiotic-induced fecal SCFA and microbiota composition disruptions. We conducted a randomized, allocation-concealed, controlled trial of amoxicillin/clavulanate administration (days 1-7), in conjunction with either BB-12-containing or control yogurt (days 1-14). We measured the fecal levels of SCFAs and bacterial composition at baseline and days 7, 14, 21, and 30. Forty-two participants were randomly assigned to the BB-12 group, and 20 participants to the control group. Antibiotic treatment suppressed the fecal acetate levels in both the control and probiotic groups. Following the cessation of antibiotics, the fecal acetate levels in the probiotic group increased over the remainder of the study and returned to the baseline levels on day 30 (-1.6% baseline), whereas, in the control group, the acetate levels remained suppressed. Further, antibiotic treatment reduced the Shannon diversity of the gut microbiota, for all the study participants at day 7. The magnitude of this change was larger and more sustained in the control group compared to the probiotic group, which is consistent with the hypothesis that BB-12 enhanced microbiota recovery. There were no significant baseline clinical differences between the two groups. Concurrent administration of amoxicillin/clavulanate and BB-12 yogurt, to healthy subjects, was associated with a significantly smaller decrease in the fecal SCFA levels and a more stable taxonomic profile of the microbiota over time than the control group.
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Affiliation(s)
- Daniel Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
- Department of Human Science, School of Nursing and Health Studies, Georgetown University Medical Center, Washington, DC 20057, USA
- Correspondence: (D.M.); (C.M.F.); (M.A.K.); Tel.: +1-202-687-2745 (D.M.); +1-410-706-3879 (C.M.F.); +1-410-706-5097 (M.A.K.)
| | - Claire M. Fraser
- Institute for Genomic Sciences, Departments of Medicine and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.G.-B.); (O.A.M.)
- Correspondence: (D.M.); (C.M.F.); (M.A.K.); Tel.: +1-202-687-2745 (D.M.); +1-410-706-3879 (C.M.F.); +1-410-706-5097 (M.A.K.)
| | - Robert F. Roberts
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Tian Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA;
| | - Silvia Grant-Beurmann
- Institute for Genomic Sciences, Departments of Medicine and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.G.-B.); (O.A.M.)
| | - Tina P. Tan
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
| | - Keisha Herbin Smith
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
| | - Tom Cronin
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
| | - Olivia A. Martin
- Institute for Genomic Sciences, Departments of Medicine and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.G.-B.); (O.A.M.)
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Sean C. Lucan
- Department of Family and Social Medicine, Albert Einstein College of Medicine, Montefiore Health System, Bronx, NY 10461, USA;
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA;
- Correspondence: (D.M.); (C.M.F.); (M.A.K.); Tel.: +1-202-687-2745 (D.M.); +1-410-706-3879 (C.M.F.); +1-410-706-5097 (M.A.K.)
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Trent M, Perin J, Rowell J, Shah M, Anders J, Matson P, Brotman RM, Ravel J, Sharps P, Rothman R, Yusuf HE, Gaydos CA. Using Innovation to Address Adolescent and Young Adult Health Disparities in Pelvic Inflammatory Disease: Design of the Technology Enhanced Community Health Precision Nursing (TECH-PN) Trial. J Infect Dis 2021; 224:S145-S151. [PMID: 34396402 DOI: 10.1093/infdis/jiab157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
New approaches to pelvic inflammatory disease (PID) care among adolescents and young adults (AYAs) that optimize self-care and personalize treatment are warranted to address age and racial-ethnic PID-related health disparities. Here we describe the 13-month preliminary feasibility and acceptability outcomes of recruitment, retention, and intervention delivery for Technology Enhanced Community Health Precision Nursing (TECH-PN) randomized controlled trial. Urban AYAs 13-25 years assigned female sex at birth with acute mild-moderate PID provided baseline and follow-up interview data and vaginal specimens for sexually transmitted infection (STI), cytokine, and microbiota assessment. All participants received medications and text-messaging support. Participants were block randomized to either control or intervention. Control participants received 1 community nursing visit with self-management for interim care per national guidelines. Intervention participants received unlimited precision care services driven by interim STI and macrolide resistance testing results by an advanced practice provider. In the first 13 months, 75.2% patients were eligible, and 76.1% of eligible patients enrolled. Of the participants, 94% completed the intervention and 96%, 91%, and 89%, respectively, completed their 14-, 30-, and 90-day visits. Baseline laboratory results revealed infection rates that were highest for Mycoplasma genitalium (45%) followed by Chlamydia trachomatis (31%). Preliminary enrollment, STI, intervention delivery, and retention data demonstrate the feasibility and acceptability of the TECH-PN intervention and support rationale for precision care for PID among urban AYAs. ClinicalTrials.gov Identifier. NCT03828994.
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Affiliation(s)
- Maria Trent
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jamie Perin
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Julia Rowell
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maunank Shah
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jennifer Anders
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pamela Matson
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Phyllis Sharps
- Department of Acute and Chronic Care, School of Nursing, Johns Hopkins University, Baltimore, Maryland, USA
| | - Richard Rothman
- Department of Emergency Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hasiya E Yusuf
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Charlotte A Gaydos
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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Lundberg DS, Pramoj Na Ayutthaya P, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D. Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 2021; 10:e66186. [PMID: 34292157 PMCID: PMC8387020 DOI: 10.7554/elife.66186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
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Affiliation(s)
- Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | | | - Annett Strauß
- Department of Evolutionary Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Wen-Sui Lo
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Thomas Lahaye
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
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Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. mSystems 2021; 6:e0029421. [PMID: 34254828 PMCID: PMC8409480 DOI: 10.1128/msystems.00294-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.
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