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Kelly LA, Yost CK, Cooke SJ. Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research. JOURNAL OF FISH BIOLOGY 2024; 104:912-919. [PMID: 38226503 DOI: 10.1111/jfb.15650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.
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Affiliation(s)
- Lisa A Kelly
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Christopher K Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
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2
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Li JG, Gao LL, Wang CC, Tu JM, Chen WH, Wu XL, Wu JX. Colonization of multidrug-resistant Gram-negative bacteria increases risk of surgical site infection after hemorrhoidectomy: a cross-sectional study of two centers in southern China. Int J Colorectal Dis 2023; 38:243. [PMID: 37779168 PMCID: PMC10543959 DOI: 10.1007/s00384-023-04535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
PURPOSE The present study aims to determine the rectoanal colonization rate and risk factors for the colonization of present multidrug-resistant bacteria (MDRBs). In addition, the relationship between MDRB colonization and surgical site infection (SSI) following hemorrhoidectomy was explored. METHODS A cross-sectional study was conducted in the Department of Colorectal Surgery of two hospitals. Patients with hemorrhoid disease, who underwent hemorrhoidectomy, were included. The pre-surgical screening of multidrug-resistant Gram-negative bacteria (MDR-GNB) colonization was performed using rectal swabs on the day of admission. Then, the MDRB colonization rate was determined through the rectal swab. Logistic regression models were established to determine the risk factors for MDRB colonization and SSI after hemorrhoidectomy. A p-value of < 0.05 was considered statistically significant. RESULTS A total of 432 patients met the inclusion criteria, and the MDRB colonization prevalence was 21.06% (91/432). The independent risk factors for MDRB colonization were as follows: patients who received ≥ 2 categories of antibiotic treatment within 3 months (odds ratio (OR): 3.714, 95% confidence interval (CI): 1.436-9.605, p = 0.007), patients with inflammatory bowel disease (IBD; OR: 6.746, 95% CI: 2.361-19.608, p < 0.001), and patients with high serum uric acid (OR: 1.006, 95% CI: 1.001-1.010, p = 0.017). Furthermore, 41.57% (37/89) of MDRB carriers and 1.81% (6/332) of non-carriers developed SSIs, with a total incidence of 10.21% (43/421). Based on the multivariable model, the rectoanal colonization of MDRBs (OR: 32.087, 95% CI: 12.052-85.424, p < 0.001) and hemoglobin < 100 g/L (OR: 4.130, 95% CI: 1.556-10.960, p = 0.004) were independently associated with SSI after hemorrhoidectomy. CONCLUSION The rectoanal colonization rate of MDRBs in hemorrhoid patients is high, and this was identified as an independent risk factor for SSI after hemorrhoidectomy.
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Affiliation(s)
- Jian-Guo Li
- Department of Colorectal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Li-Lian Gao
- Department of Colorectal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Cun-Chuan Wang
- Department of Colorectal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, 510630, China.
| | - Jia-Min Tu
- Department of Colorectal Surgery, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen, China
| | - Wen-Hui Chen
- Department of Colorectal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Xiang-Lin Wu
- Department of Colorectal Surgery, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen, China
| | - Jin-Xia Wu
- Department of Colorectal Surgery, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen, China
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Graspeuntner S, Lupatsii M, Dashdorj L, Rody A, Rupp J, Bossung V, Härtel C. First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes. Microbiol Spectr 2023; 11:e0525422. [PMID: 37097170 PMCID: PMC10269712 DOI: 10.1128/spectrum.05254-22] [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: 12/22/2022] [Accepted: 04/10/2023] [Indexed: 04/26/2023] Open
Abstract
The human gut microbiome plays a vital role in health and disease. In particular, the first days of life provide a unique window of opportunity for development and establishment of microbial community. Currently, stool samples are known to be the most widely used sampling approach for studying the gut microbiome. However, complicated sample acquisition at certain time points, challenges in transportation, and patient discomfort underline the need for development of alternative sampling approaches. One of the alternatives is rectal swabs, shown to be a reliable proxy for gut microbiome analysis when obtained from adults. Here, we compare the usability of rectal swabs and meconium paired samples collected from infants on the first days of life. Our results indicate that the two sampling approaches display significantly distinct patterns in microbial composition and alpha and beta diversity as well as detection of resistance genes. Moreover, the dissimilarity between the two collection methods was greater than the interindividual variation. Therefore, we conclude that rectal swabs are not a reliable proxy compared to stool samples for gut microbiome analysis when collected on the first days of a newborn's life. IMPORTANCE Currently, there are numerous suggestions on how to ease the notoriously complex and error-prone methodological setups to study the gut microbiota of newborns during the first days of life. Especially, meconium samples are regularly failing to yield meaningful data output and therefore have been suggested to be replaced by rectal swabs as done in adults as well. We find this development toward a simplified method to be producing dramatically erroneous results, skewing data interpretation away from the real aspects to be considered for neonatal health during the first days of life. We have put together our knowledge on this critical aspect with careful consideration and identified the failure of rectal swabs to be a replacement for sampling of meconium in term-born newborns.
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Affiliation(s)
- S. Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - M. Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - L. Dashdorj
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - A. Rody
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - J. Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - V. Bossung
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Lübeck, Germany
- Department of Pediatrics, University Hospital of Würzburg, Würzburg, Germany
| | - C. Härtel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Department of Obstetrics, University Hospital of Zurich, Zurich, Switzerland
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4
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Bongers KS, Chanderraj R, Woods RJ, McDonald RA, Adame MD, Falkowski NR, Brown CA, Baker JM, Winner KM, Fergle DJ, Hinkle KJ, Standke AK, Vendrov KC, Young VB, Stringer KA, Sjoding MW, Dickson RP. The Gut Microbiome Modulates Body Temperature Both in Sepsis and Health. Am J Respir Crit Care Med 2023; 207:1030-1041. [PMID: 36378114 PMCID: PMC10112447 DOI: 10.1164/rccm.202201-0161oc] [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: 01/23/2022] [Accepted: 11/15/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Among patients with sepsis, variation in temperature trajectories predicts clinical outcomes. In healthy individuals, normal body temperature is variable and has decreased consistently since the 1860s. The biologic underpinnings of this temperature variation in disease and health are unknown. Objectives: To establish and interrogate the role of the gut microbiome in calibrating body temperature. Methods: We performed a series of translational analyses and experiments to determine whether and how variation in gut microbiota explains variation in body temperature in sepsis and in health. We studied patient temperature trajectories using electronic medical record data. We characterized gut microbiota in hospitalized patients using 16S ribosomal RNA gene sequencing. We modeled sepsis using intraperitoneal LPS in mice and modulated the microbiome using antibiotics, germ-free, and gnotobiotic animals. Measurements and Main Results: Consistent with prior work, we identified four temperature trajectories in patients hospitalized with sepsis that predicted clinical outcomes. In a separate cohort of 116 hospitalized patients, we found that the composition of patients' gut microbiota at admission predicted their temperature trajectories. Compared with conventional mice, germ-free mice had reduced temperature loss during experimental sepsis. Among conventional mice, heterogeneity of temperature response in sepsis was strongly explained by variation in gut microbiota. Healthy germ-free and antibiotic-treated mice both had lower basal body temperatures compared with control animals. The Lachnospiraceae family was consistently associated with temperature trajectories in hospitalized patients, experimental sepsis, and antibiotic-treated mice. Conclusions: The gut microbiome is a key modulator of body temperature variation in both health and critical illness and is thus a major, understudied target for modulating physiologic heterogeneity in sepsis.
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Affiliation(s)
| | - Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Medicine Service, Infectious Diseases Section, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Robert J. Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Medicine Service, Infectious Diseases Section, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
- Center for Computational Medicine and Bioinformatics and
| | | | - Mark D. Adame
- Division of Pulmonary and Critical Care Medicine and
| | | | - Christopher A. Brown
- Division of Pulmonary and Critical Care Medicine and
- Institute for Research on Innovation and Science, Institute for Social Research
| | - Jennifer M. Baker
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, Medical School
| | - Katherine M. Winner
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, Medical School
| | | | | | - Alexandra K. Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
| | - Kimberly C. Vendrov
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Department of Microbiology and Immunology, Medical School
| | - Kathleen A. Stringer
- Division of Pulmonary and Critical Care Medicine and
- Department of Clinical Pharmacy, College of Pharmacy, and
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, Michigan
| | - Michael W. Sjoding
- Division of Pulmonary and Critical Care Medicine and
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan; and
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, Michigan
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, Medical School
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan; and
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Evans T, Ali U, Anderton R, Raby E, Manning L, Litton E. Lower gut dysbiosis and mortality in acute critical illness: a systematic review and meta-analysis. Intensive Care Med Exp 2023; 11:6. [PMID: 36732439 PMCID: PMC9895325 DOI: 10.1186/s40635-022-00486-z] [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: 10/26/2022] [Accepted: 12/17/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The human gastrointestinal tract harbours a complex multi-kingdom community known as the microbiome. Dysbiosis refers to its disruption and is reportedly extreme in acute critical illness yet its clinical implications are unresolved. The review systematically evaluates the association between gut dysbiosis and clinical outcomes of patients early in critical illness. METHODS Following PRISMA guidelines, a prospectively registered search was undertaken of MEDLINE and Cochrane databases for observational studies undertaking metagenomic sequencing of the lower gastrointestinal tract of critically ill adults and children within 72 h of admission. Eligible studies reported an alpha diversity metric and one or more of the primary outcome, in-hospital mortality, or secondary clinical outcomes. After aggregate data were requested, meta-analysis was performed for four studies with in-hospital mortality stratified to high or low Shannon index. RESULTS The search identified 26 studies for systematic review and 4 had suitable data for meta-analysis. No effect of alpha diversity was seen on in-hospital mortality after binary transformation of Shannon index (odds ratio 0.52, CI 0.12-4.98, I2 = 0.64) however certainty of evidence is low. Pathogen dominance and commensal depletion were each more frequently associated with in-hospital mortality, adverse clinical and ecological sequelae, particularly overabundance of Enterococcus. CONCLUSIONS There is a paucity of large, rigorous observational studies in this population. Globally, alpha diversity was dynamically reduced in early ICU admission in adults and children and was not associated with in-hospital mortality. The abundance of taxa such as Enterococcus spp. appears to offer greater predictive capacity for important clinical and ecological outcomes.
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Affiliation(s)
- Tess Evans
- grid.459958.c0000 0004 4680 1997Intensive Care Unit, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Umar Ali
- grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Ryan Anderton
- grid.266886.40000 0004 0402 6494School of Health Sciences, University of Notre Dame Australia (Fremantle), Fremantle, Australia
| | - Edward Raby
- grid.459958.c0000 0004 4680 1997Department of Infectious Diseases, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Laurens Manning
- grid.459958.c0000 0004 4680 1997Department of Infectious Diseases, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
| | - Edward Litton
- grid.459958.c0000 0004 4680 1997Intensive Care Unit, Fiona Stanley Hospital, South Metropolitan Health Service, WA Health, Perth, Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Nedlands, Australia
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6
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Rectal swabs as a viable alternative to faecal sampling for the analysis of gut microbiota functionality and composition. Sci Rep 2023; 13:493. [PMID: 36627399 PMCID: PMC9831010 DOI: 10.1038/s41598-022-27131-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Faecal or biopsy samples are frequently used to analyse the gut microbiota, but issues remain with the provision and collection of such samples. Rectal swabs are widely-utilised in clinical practice and previous data demonstrate their potential role in microbiota analyses; however, studies to date have been heterogenous, and there are a particular lack of data concerning the utility of swabs for the analysis of the microbiota's functionality and metabolome. We compared paired stool and rectal swab samples from healthy individuals to investigate whether rectal swabs are a reliable proxy for faecal sampling. There were no significant differences in key alpha and beta diversity measures between swab and faecal samples, and inter-subject variability was preserved. Additionally, no significant differences were demonstrated in abundance of major annotated phyla. Inferred gut functionality using Tax4Fun2 showed excellent correlation between the two sampling techniques (Pearson's coefficient r = 0.9217, P < 0.0001). Proton nuclear magnetic resonance (1H NMR) spectroscopy enabled the detection of 20 metabolites, with overall excellent correlation identified between rectal swab and faecal samples for levels all metabolites collectively, although more variable degrees of association between swab and stool for levels of individual metabolites. These data support the utility of rectal swabs in both compositional and functional analyses of the gut microbiota.
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7
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Shahi F, Forrester S, Redeker K, Chong JP, Barlow G. Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year. Wellcome Open Res 2022; 7:50. [PMID: 36874581 PMCID: PMC9975432 DOI: 10.12688/wellcomeopenres.17450.3] [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] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global concern and better understanding of the gut microbiome, a known 'amplifier' of AMR, may allow future clinicians to tailor therapy to minimise this risk and offer a personalised medicine approach. To examine the gut microbiome, patients are required to provide faecal samples; more convenient and cheaper solutions need to be found. METHODS As part of a pilot study looking at how routes of administration affect the gut microbiome in NHS patients undergoing routine clinical management for infections, we hypothesised that effects on the gut microbiome varied with the route and metabolism of antibiotic used, and these changes may be reflected in breath metabolites. We present a case report of a patient with an unusual clinical history, alongside breath metabolite and gut microbiome data taken before, during and after antibiotic therapy over a period of one year. RESULTS We noted a shift in the dominant Bacteroides strain in the patient's gut microbiome between pre- and post-therapy samples, along with an alteration in the composition of breath metabolites. CONCLUSIONS This study provides a framework for similar future work and highlights the need for further research on the relationships between changes in microbial gut communities and antimicrobial exposure, patient clinical status, and the metabolites of human breath.
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Affiliation(s)
- Farah Shahi
- Department of Biology, University of York, UK, York, YO10 5DD, UK
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, HU3 2JZ, UK
| | - Sarah Forrester
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - Kelly Redeker
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - James P.J. Chong
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - Gavin Barlow
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, HU3 2JZ, UK
- Experimental Medicine and Biomedicine, Hull York Medical School, University of York, York, YO10 5DD, UK
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Mj O, Turner GA, A S, Frizelle FA, R P. Distinct changes in the colonic microbiome associated with acute diverticulitis. Colorectal Dis 2022; 24:1591-1601. [PMID: 35950499 PMCID: PMC10087140 DOI: 10.1111/codi.16271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 01/07/2023]
Abstract
AIM The pathogenesis of acute diverticulitis (AD) remains incompletely understood, despite it being one of the most common gastrointestinal conditions worldwide. The aim of this study was to investigate the role of the colonic microbiome in the pathogenesis of AD. METHOD A prospective case-control study was performed, comparing the microbiome of AD patients with that of controls, using 16S rRNA sequencing of rectal swab samples. RESULTS The microbiome of individuals with AD showed lower diversity than that of controls. There were significant compositional differences observed, with a lower abundance of commensal bacterial families and genera such as Lachnospiraceae, Ruminococcus and Faecalibacterium in AD patients compared with controls, and there was an increase in several genera with known pathogenic roles including Fusobacteria, Prevotella and Paraprevotella. CONCLUSION This is the largest study to date to examine the microbiota of AD patients, and adds evidence to the proposed hypothesis that alterations in the colonic microbiome play a role in the pathogenesis of AD.
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Affiliation(s)
- O'Grady Mj
- Whanganui Hospital, Wanganui, New Zealand
| | - Greg A Turner
- Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sulit A
- University of Otago, Christchurch, New Zealand
| | - Frank A Frizelle
- University of Otago, Christchurch, New Zealand.,Christchurch Hospital, Christchurch, New Zealand
| | - Purcell R
- University of Otago, Christchurch, New Zealand
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Liss MA, Garg H, Sokurenko EV, Patterson JE, Wickes BL. Molecular genetic testing does not improve the detection of fluoroquinolone resistance before transrectal prostate biopsy. Prostate Int 2022; 10:194-199. [PMID: 36570643 PMCID: PMC9747570 DOI: 10.1016/j.prnil.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/02/2022] [Accepted: 06/30/2022] [Indexed: 12/27/2022] Open
Abstract
Background Fluoroquinolone-resistant (FQR) Escherichia coli (E. coli) causes transrectal prostate biopsy infections. We seek to further identify fluoroquinolones resistance by the incorporation of genetic profiling to influence antibiotic selection for transrectal prostate biopsy and whether the addition of this genetic testing could improve the prediction of FQR detection at the time of biopsy. Materials and methods In this prospective observational cohort study, rectal swabs were collected within 30 days of an upcoming prostate biopsy. These swabs were sent for phenotypic and genotypic assessment to predict FQR on the day of the biopsy. Phenotype: Specimens were inoculated onto MacConkey agar containing ciprofloxacin using standard culture techniques to determine FQR status. Genotype: We compared cultures to polymerase chain reaction (PCR) sequence typing (E.coli- ST131/H30/ST69) and bacterial plasmids (gyrA, qnrQ, and qnrS). The presence of FQR on this testing was compared to the second rectal swab collected just before biopsy (2 hours after ciprofloxacin prophylaxis), which served as the gold standard for FQR. Results Overall, the FQR rate was 23.6%. The bacterial plasmids (qnr) were present in 54.1% of samples, and multidrug-resistant E. coli ST131 was present in 12.5% of samples. In comparison, phenotypic assessment using rectal culture had a better prediction for the presence of FQR as compared to genotypic testing [area under the curve (AUC) = 0.85 in phenotype arm vs. AUC = 0.45 in genotype arm]. Conclusion We detected a high prevalence of FQR genes in the rectum, but the addition of PCR-based genotyping did not improve the prediction of culture-based FQR at the time of biopsy.
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Affiliation(s)
- Michael A. Liss
- University of Texas Health San Antonio Long School of Medicine, Department of Urology, USA
- South Texas Veterans Healthcare System, San Antonio, TX, USA
| | - Harshit Garg
- University of Texas Health San Antonio Long School of Medicine, Department of Urology, USA
| | | | - Jan E. Patterson
- University of Texas Health San Antonio Long School of Medicine, Department of Medicine, USA
| | - Brian L. Wickes
- University of Texas Health San Antonio Long School of Medicine, Department of Microbiology, Immunology, and Molecular Genetics, USA
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10
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Relationship between mucosa-associated gut microbiota and human diseases. Biochem Soc Trans 2022; 50:1225-1236. [PMID: 36214382 PMCID: PMC9704521 DOI: 10.1042/bst20201201] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022]
Abstract
The mucus layer covering the gastrointestinal (GI) tract plays a critical role in maintaining gut homeostasis. In the colon, the inner mucus layer ensures commensal microbes are kept at a safe distance from the epithelium while mucin glycans in the outer mucus layer provide microbes with nutrients and binding sites. Microbes residing in the mucus form part of the so-called 'mucosa-associated microbiota' (MAM), a microbial community which, due to its close proximity to the epithelium, has a profound impact on immune and metabolic health by directly impacting gut barrier function and the immune system. Alterations in GI microbial communities have been linked to human diseases. Although most of this knowledge is based on analysis of the faecal microbiota, a growing number of studies show that the MAM signature differs from faecal or luminal microbiota and has the potential to be used to distinguish between diseased and healthy status in well-studied conditions such as IBD, IBS and CRC. However, our knowledge about spatial microbial alterations in pathogenesis remains severely hampered by issues surrounding access to microbial communities in the human gut. In this review, we provide state-of-the-art information on how to access MAM in humans, the composition of MAM, and how changes in MAM relate to changes in human health and disease. A better understanding of interactions occurring at the mucosal surface is essential to advance our understanding of diseases affecting the GI tract and beyond.
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Alrahawy M, Javed S, Atif H, Elsanhoury K, Mekhaeil K, Eskander G. Microbiome and Colorectal Cancer Management. Cureus 2022; 14:e30720. [DOI: 10.7759/cureus.30720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
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Patrier J, Villageois-Tran K, Szychowiak P, Ruckly S, Gschwind R, Wicky PH, Gueye S, Armand-Lefevre L, Marzouk M, Sonneville R, Bouadma L, Petitjean M, Lamara F, de Montmollin E, Timsit JF, Ruppé E. Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults. Crit Care 2022; 26:300. [PMID: 36192756 PMCID: PMC9527714 DOI: 10.1186/s13054-022-04164-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The composition of the digestive microbiota may be associated with outcome and infections in patients admitted to the intensive care unit (ICU). The dominance by opportunistic pathogens (such as Enterococcus) has been associated with death. However, whether this association remains all throughout the hospitalization are lacking. METHODS We performed a single-center observational prospective cohort study in critically ill patients admitted with severe SARS-CoV-2 infection. Oropharyngeal and rectal swabs were collected at admission and then twice weekly until discharge or death. Quantitative cultures for opportunistic pathogens were performed on oropharyngeal and rectal swabs. The composition of the intestinal microbiota was assessed by 16S rDNA sequencing. Oropharyngeal and intestinal concentrations of opportunistic pathogens, intestinal richness and diversity were entered into a multivariable Cox model as time-dependent covariates. The primary outcome was death at day 90. RESULTS From March to September 2020, 95 patients (765 samples) were included. The Simplified Acute Physiology Score 2 (SAPS 2) at admission was 33 [24; 50] and a Sequential Organ Failure Assessment score (SOFA score) at 6 [4; 8]. Day 90 all-cause mortality was 44.2% (42/95). We observed that the oropharyngeal and rectal concentrations of Enterococcus spp., Staphylococcus aureus and Candida spp. were associated with a higher risk of death. This association remained significant after adjustment for prognostic covariates (age, chronic disease, daily antimicrobial agent use and daily SOFA score). A one-log increase in Enterococcus spp., S. aureus and Candida spp. in oropharyngeal or rectal swabs was associated with a 17% or greater increase in the risk of death. CONCLUSION We found that elevated oropharyngeal/intestinal Enterococcus spp. S. aureus and Candida spp. concentrations, assessed by culture, are associated with mortality, independent of age, organ failure, and antibiotic therapy, opening prospects for simple and inexpensive microbiota-based markers for the prognosis of critically ill SARS-CoV-2 patients.
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Affiliation(s)
- Juliette Patrier
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France
| | - Khanh Villageois-Tran
- grid.411599.10000 0000 8595 4540AP-HP, Service de Microbiologie, Hôpital Beaujon, 75018 Paris, France ,grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Piotr Szychowiak
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France ,grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Stéphane Ruckly
- grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.508487.60000 0004 7885 7602OUTCOME REA Research Network, IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Rémi Gschwind
- grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Paul-Henri Wicky
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France
| | - Signara Gueye
- grid.411119.d0000 0000 8588 831XAP-HP, Service de Bactériologie, Hôpital Bichat-Claude Bernard, 75018 Paris, France
| | - Laurence Armand-Lefevre
- grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.411119.d0000 0000 8588 831XAP-HP, Service de Bactériologie, Hôpital Bichat-Claude Bernard, 75018 Paris, France
| | - Mehdi Marzouk
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France
| | - Romain Sonneville
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France ,grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.508487.60000 0004 7885 7602OUTCOME REA Research Network, IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Lila Bouadma
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France ,grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.508487.60000 0004 7885 7602OUTCOME REA Research Network, IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Marie Petitjean
- grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Fariza Lamara
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France ,grid.508487.60000 0004 7885 7602OUTCOME REA Research Network, IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Etienne de Montmollin
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France ,grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.508487.60000 0004 7885 7602OUTCOME REA Research Network, IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Jean-Francois Timsit
- grid.411119.d0000 0000 8588 831XAP-HP, Bichat Hospital, Medical and Infectious Diseases ICU (MI2), 75018 Paris, France ,grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.508487.60000 0004 7885 7602OUTCOME REA Research Network, IAME, INSERM, Université de Paris, 75018 Paris, France
| | - Etienne Ruppé
- grid.508487.60000 0004 7885 7602IAME, INSERM, Université de Paris, 75018 Paris, France ,grid.411119.d0000 0000 8588 831XAP-HP, Service de Bactériologie, Hôpital Bichat-Claude Bernard, 75018 Paris, France
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13
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Guang Y, Shen X, Tan Y, Tang S, Chen J, Zhang L, Wang B, Ye S, Chen X, Yang C, Chen C, Li G, Chen J, Cui X, Lin W, Wang X, Fang G. Systematic analysis of microbiota in pregnant Chinese women and its association with miscarriage. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1099. [PMID: 36388813 PMCID: PMC9652576 DOI: 10.21037/atm-22-4115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/08/2022] [Indexed: 08/13/2023]
Abstract
BACKGROUND Miscarriage is the most common adverse pregnancy outcome and more than 50% of its incidence remains unexplained. Earlier studies have suggested that maternal microbiota might be associated with miscarriage, but the association is insufficiently understood. METHODS We used 16S ribosomal RNA (rRNA) amplicon sequencing and metagenomic sequencing technology to characterize the bacterial composition of three sites including the rectum, vagina, and cervix of a case group of 63 pregnant women who had miscarried compared to a control group of 24 pregnant women who underwent voluntary elective abortion. RESULTS The alpha-diversity from the rectum and cervix was significantly decreased in the case group relative to the control group. However, we did not find significant differences in microbial diversity of vaginal samples between the two groups. Lactobacillus was the most predominant genus in the cervix and vaginal samples. Gestational age at the time of surgery was positively associated with the rectum microbiota diversity, with an effect size of 10% (P=0.004). Host factors including gestational age and red blood count (RBC) were associated with the rectal microbiota diversity. CONCLUSIONS We detected a significantly lower rectal microbiota diversity and a pro-inflammatory tendency in the miscarriage group. This is the first study to investigate the association of microbiota from samples collected from three sites and miscarriage. Further studies are warranted to explore further the role of microbiota in miscarriage.
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Affiliation(s)
- Yu Guang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
| | - Xiao Shen
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
| | - Yan Tan
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
| | - Shanmei Tang
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Jing Chen
- The School of Nursing, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Longhui Zhang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Baohong Wang
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
| | - Suyan Ye
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
| | - Xiaomei Chen
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
| | - Chuanchun Yang
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Chuan Chen
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Guanglei Li
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Jianguo Chen
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Xiaoli Cui
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Weisheng Lin
- CheerLand Biological Technology Co., Ltd., Shenzhen, China
| | - Xuelai Wang
- The School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Guangguang Fang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- Department of Gynecology, Shenzhen Dapeng New District Maternal and Child Health Hospital, Shenzhen, China
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14
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Geldenhuys J, Redelinghuys MJ, Lombaard HA, Ehlers MM, Cowan D, Kock MM. Diversity of the gut, vaginal and oral microbiome among pregnant women in South Africa with and without pre-eclampsia. Front Glob Womens Health 2022; 3:810673. [PMID: 36188424 PMCID: PMC9525020 DOI: 10.3389/fgwh.2022.810673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Changes in microbial communities are a known characteristic of various inflammatory diseases and have been linked to adverse pregnancy outcomes, such as preterm birth. However, there is a paucity of information regarding the taxonomic composition and/or diversity of microbial communities in pre-eclampsia. The aim of this study was to determine the diversity of the gut, vaginal and oral microbiome in a cohort of South African pregnant women with and without pre-eclampsia. The diversity of the gut, vaginal and oral microbiome was determined by targeted next generation sequencing (NGS) of the V3 and V4 region of the 16S rRNA gene on the Illumina MiSeq platform. Results In this study population, pre-eclampsia was associated with a significantly higher alpha diversity (P = 0.0472; indicated by the Shannon index) in the vaginal microbiome accompanied with a significant reduction in Lactobacillus spp. (P = 0.0275), compared to normotensive pregnant women. Lactobacillus iners was identified as the predominant species of the vaginal microbiome in both cohorts. High inter-individual variation in alpha diversity was observed in the gut and oral microbiome in both cohorts. Although differences in the relative abundance of bacteria at all phylogenetic levels were observed, overall microbial composition of the gut, oral and vaginal microbiome was not significantly different in the pre-eclampsia cohort compared to the normotensive cohort. Conclusion Collectively, a reduction of Lactobacillus spp., and predominance of L. iners in pregnant women with pre-eclampsia could suggest an unstable vaginal microbiome that might predispose pregnant women to develop pre-eclampsia. The lack of significant structural changes in the gut, oral and vaginal microbiome does not suggest that the characterized communities play a role in pre-eclampsia, but could indicate a characteristic unique to the study population. The current study provided novel information on the diversity of the gut, oral and vaginal microbiome among pregnant women in South Africa with and without pre-eclampsia. The current study provides a baseline for further investigations on the potential role of microbial communities in pre-eclampsia.
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Affiliation(s)
- Janri Geldenhuys
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Mathys J. Redelinghuys
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Hendrik A. Lombaard
- Obstetrics and Gynecology, Rahima Moosa Mother and Child Hospital, Wits Obstetrics and Gynecology Clinical Research Division, School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Marthie M. Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Marleen M. Kock
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
- *Correspondence: Marleen M. Kock
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Hussan H, Abu Dayyeh BK, Chen J, Johnson S, Riedl KM, Grainger EM, Brooks J, Hinton A, Simpson C, Kashyap PC. Adjustable Intragastric Balloon Leads to Significant Improvement in Obesity-Related Lipidome and Fecal Microbiome Profiles: A Proof-of-Concept Study. Clin Transl Gastroenterol 2022; 13:e00508. [PMID: 35905412 PMCID: PMC10476793 DOI: 10.14309/ctg.0000000000000508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Intragastric balloons (IGBs) are a safe and effective treatment for obesity. However, limited knowledge exists on the underlying biological changes with IGB placement. METHODS This single-institution study was part of an adjustable IGB randomized controlled trial. Subjects with obesity were randomized in a 2 is to 1 ratio to 32 weeks of IGB with diet/exercise counseling (n = 8) vs counseling alone (controls, n = 4). Diet/exercise counseling was continued for 24 weeks post-IGB removal to assess weight maintenance. We used mass spectrometry for nontargeted plasma lipidomics analysis and 16S rRNA sequencing to profile the fecal microbiome. RESULTS Subjects with IGBs lost 15.5% of their body weight at 32 weeks vs 2.59% for controls (P < 0.05). Maintenance of a 10.5% weight loss occurred post-IGB explant. IGB placement, followed by weight maintenance, led to a -378.9 μM/L reduction in serum free fatty acids compared with pre-IGB (95% confidence interval: 612.9, -145.0). This reduction was mainly in saturated, mono, and omega-6 fatty acids when compared with pre-IGB. Polyunsaturated phosphatidylcholines also increased after IGB placement (difference of 27 μM/L; 95% confidence interval: 1.1, 52.8). Compared with controls, saturated and omega-6 free fatty acids (linoleic and arachidonic acids) were reduced after IGB placement. The fecal microbiota changed post-IGB placement and weight maintenance vs pre-IGB (P < 0.05). Further analysis showed a possible trend toward reduced Firmicutes and increased Bacteroidetes post-IGB and counseling, a change that was not conclusively different from counseling alone. DISCUSSION IGB treatment is associated with an altered fecal microbiome profile and may have a better effect on obesity-related lipidome than counseling alone.
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Affiliation(s)
- Hisham Hussan
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Barham K. Abu Dayyeh
- Division of Gastroenterology, University of California Davis, Sacramento, CA, USA
| | - Jun Chen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen Johnson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ken M. Riedl
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Elizabeth M. Grainger
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeffrey Brooks
- Division of Medical Oncology, The Ohio State University, Columbus, Ohio, USA
| | | | - Christina Simpson
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Purna C. Kashyap
- Division of Gastroenterology, University of California Davis, Sacramento, CA, USA
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Koyande N, Gangopadhyay M, Thatikonda S, Rengan AK. The role of gut microbiota in the development of colorectal cancer: a review. Int J Colorectal Dis 2022; 37:1509-1523. [PMID: 35704091 DOI: 10.1007/s00384-022-04192-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/21/2022] [Indexed: 02/04/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is the cancer of the colon and rectum. Recent research has found a link between CRC and human gut microbiota. This review explores the effect of gut microbiota on colorectal carcinogenesis and the development of chemoresistance. METHODS A literature overview was performed to identify the gut microbiota species that showed altered abundance in CRC patients and the mechanisms by which some of them aid in the development of chemoresistance. RESULTS Types of gut microbiota present and methods of analyzing them were discussed. We observed that numerous microbiota showed altered abundance in CRC patients and could act as a biomarker for CRC diagnosis and treatment. Further, it was demonstrated that microbes also have a role in the development of chemoresistance by mechanisms like immune system activation, drug modification, and autophagy modulation. Finally, the key issue of the growing global problem of antimicrobial resistance and its relationship with CRC was highlighted. CONCLUSION This review discussed the role of gut microbiota dysbiosis on colorectal cancer progression and the development of chemoresistance.
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Affiliation(s)
- Navami Koyande
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India
| | - Madhusree Gangopadhyay
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India
| | - Shashidhar Thatikonda
- Department of Civil Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India
| | - Aravind Kumar Rengan
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India.
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17
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Shahi F, Forrester S, Redeker K, Chong JP, Barlow G. Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year. Wellcome Open Res 2022; 7:50. [PMID: 36874581 PMCID: PMC9975432 DOI: 10.12688/wellcomeopenres.17450.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global concern and better understanding of the gut microbiome, a known 'amplifier' of AMR, may allow future clinicians to tailor therapy to minimise this risk and offer a personalised medicine approach. To examine the gut microbiome, patients are required to provide faecal samples; more convenient and cheaper solutions need to be found. METHODS As part of a pilot study looking at how routes of administration affect the gut microbiome in NHS patients undergoing routine clinical management for infections, we hypothesised that effects on the gut microbiome varied with the route and metabolism of antibiotic used, and these changes may be reflected in breath metabolites. We present a case report of a patient with an unusual clinical history, alongside breath metabolite and gut microbiome data taken before, during and after antibiotic therapy over a period of one year. RESULTS We noted a shift in the dominant Bacteroides strain in the patient's gut microbiome between pre- and post-therapy samples, along with an alteration in the composition of breath metabolites. CONCLUSIONS This study provides a framework for similar future work and highlights the need for further research on the relationships between changes in microbial gut communities and antimicrobial exposure, patient clinical status, and the metabolites of human breath.
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Affiliation(s)
- Farah Shahi
- Department of Biology, University of York, UK, York, YO10 5DD, UK
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, HU3 2JZ, UK
| | - Sarah Forrester
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - Kelly Redeker
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - James P.J. Chong
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - Gavin Barlow
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, HU3 2JZ, UK
- Experimental Medicine and Biomedicine, Hull York Medical School, University of York, York, YO10 5DD, UK
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18
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Watkins CA, Gaines T, Strathdee F, Baily JL, Watson E, Hall AJ, Free A, Dagleish MP. A comparative study of the fecal microbiota of gray seal pups and yearlings ‐ a marine mammal sentinel species. Microbiologyopen 2022; 11:e1281. [PMID: 35765184 PMCID: PMC9126079 DOI: 10.1002/mbo3.1281] [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: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Gray seals (Halichoerus grypus) can act as sentinel species reflecting the condition of the environment they inhabit. Our previous research identified strains of pathogenic Campylobacter and Salmonella, originating from both human and agricultural animal hosts, on rectal swabs from live gray seal (H. grypus) pups and yearlings on the Isle of May, Scotland, UK. We examined rectal swabs from the same pup (n = 90) and yearling (n = 19) gray seals to gain further understanding into the effects of age‐related changes (pup vs. yearling) and three different natal terrestrial habitats on seal pup fecal microbiota. DNA was extracted from a subset of rectal swabs (pups n = 23, yearlings n = 9) using an optimized procedure, and the V4 region of the 16S ribosomal RNA gene was sequenced to identify each individual's microbiota. Diversity in pup samples was lower (3.92 ± 0.19) than yearlings (4.66 ± 0.39) although not significant at the p = 0.05 level (p = 0.062) but differences in the composition of the microbiota were (p < 0.001). Similarly, differences between the composition of the microbiota from pups from three different terrestrial habitats (Pilgrim's Haven [PH], Rona Rocks [RR], and Tarbet Slope [TS]) were highly significant (p < 0.001). Pairwise tests showed significant differences between all three habitats: PH versus TS (p = 0.019), PH versus RR (p = 0.042) and TS versus RR (p = 0.020). This preliminary study suggests a general trend, that seal microbiomes are modified by both age and, in pups, different terrestrial habitats. Furthermore, knowledge of the microbiota species present has the potential to be used in determining the environmental quality index.
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Affiliation(s)
- Craig A. Watkins
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
| | - Taylor Gaines
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
| | - Fiona Strathdee
- School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Johanna L. Baily
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
- Sea Mammal Research Unit, Scottish Oceans Institute University of St Andrews St Andrews UK
| | - Eleanor Watson
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
| | - Ailsa J. Hall
- Sea Mammal Research Unit, Scottish Oceans Institute University of St Andrews St Andrews UK
| | - Andrew Free
- School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Mark P. Dagleish
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
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19
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Schlebusch S, Graham RMA, Jennison AV, Lassig-Smith MM, Harris PNA, Lipman J, Ó Cuív P, Paterson DL. Standard rectal swabs as a surrogate sample for gut microbiome monitoring in intensive care. BMC Microbiol 2022; 22:99. [PMID: 35413802 PMCID: PMC9004175 DOI: 10.1186/s12866-022-02487-0] [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: 06/07/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The purpose of this study was to investigate the use of routinely available rectal swabs as a surrogate sample type for testing the gut microbiome and monitoring antibiotic effects on key gut microorganisms, of patients hospitalised in an intensive care unit. A metagenomic whole genome sequencing approach was undertaken to determine the diversity of organisms as well as resistance genes and to compare findings between the two sampling techniques. RESULTS No significant difference was observed in overall diversity between the faeces and rectal swabs and sampling technique was not demonstrated to predict microbial community variation. More human DNA was present in the swabs and some differences were observed only for a select few anaerobes and bacteria also associated with skin and/or the female genitourinary system, possibly reflecting sampling site or technique. Antibiotics and collections at different times of admission were both considered significant influences on microbial community composition alteration. Detection of antibiotic resistance genes between rectal swabs and faeces were overall not significantly different, although some variations were detected with a potential association with the number of human sequence reads in a sample. CONCLUSION Testing the gut microbiome using standard rectal swab collection techniques currently used for multi-resistant organism screening has been demonstrated to have utility in gut microbiome monitoring in intensive care. The use of information from this article, in terms of methodology as well as near equivalence demonstrated between rectal swabs and faeces will be able to support and potentially facilitate the introduction into clinical practice.
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Affiliation(s)
- Sanmarié Schlebusch
- University of Queensland Centre for Clinical Research, Herston, Brisbane, Queensland, Australia. .,Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers Plains, Brisbane, Queensland, Australia. .,Pathology Queensland, Queensland Health, Herston, Brisbane, Queensland, Australia.
| | - Rikki M A Graham
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers Plains, Brisbane, Queensland, Australia
| | - Amy V Jennison
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers Plains, Brisbane, Queensland, Australia
| | - Melissa M Lassig-Smith
- Intensive Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Herston, Brisbane, Queensland, Australia.,Pathology Queensland, Queensland Health, Herston, Brisbane, Queensland, Australia
| | - Jeffrey Lipman
- University of Queensland Centre for Clinical Research, Herston, Brisbane, Queensland, Australia.,Intensive Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.,Jamieson Trauma Institute, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.,Nîmes University Hospital, University of Montpellier, Nîmes, France
| | - Páraic Ó Cuív
- Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Herston, Brisbane, Queensland, Australia
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20
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Abstract
Newer 'omics approaches, such as metatranscriptomics and metabolomics, allow functional assessments of the interaction(s) between the gut microbiome and the human host. However, in order to generate meaningful data with these approaches, the method of sample collection is critical. Prior studies have relied on expensive and invasive means toward sample acquisition, such as intestinal biopsy, while other studies have relied on easier methods of collection, such as fecal samples that do not necessarily represent those microbes in contact with the host. In this pilot study, we attempt to characterize a novel, minimally invasive method toward sampling the human microbiome using mucosal cytology brush sampling compared to intestinal gut biopsy samples on 5 healthy participants undergoing routine screening colonoscopy. We compared metatranscriptomic analyses between the two collection methods and identified increased taxonomic evenness and beta diversity in the cytology brush samples and similar community transcriptional profiles between the two methods. Metabolomics assessment demonstrated striking differences between the two methods, implying a difference in bacterial-derived versus human-absorbed metabolites. Put together, this study supports the use of microbiome sampling with cytology brushes, but caution must be exercised when performing metabolomics assessment, as this represents differential metabolite production but not absorption by the host. IMPORTANCE In order to generate meaningful metabolomic and microbiome data, the method of sample collection is critical. This study utilizes and compares two methods for intestinal tissue collection for evaluation of metabolites and microbiomes, finding that using a brush to sample the microbiome provides valuable data. However, for metabolomics assessment, biopsy samples may still be required.
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Wells J, Bai J, Tsementzi D, Jhaney CI, Foster A, Watkins Bruner D, Gillespie T, Li Y, Hu YJ. Exploring the Anal Microbiome in HIV Positive and High-Risk HIV Negative Women. AIDS Res Hum Retroviruses 2022; 38:228-236. [PMID: 35044233 PMCID: PMC8968844 DOI: 10.1089/aid.2020.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This exploratory study sought to characterize the anal microbiome and explore associations among the anal microbiome, risk factors for anal cancer, and clinical factors. A pilot sample of 50 HIV infected and high-risk HIV negative women were recruited from the former Women's Interagency HIV Study. Microbiome characterization by 16S rRNA gene sequencing and datasets were analyzed using QIIME 2™. Composition of the anal microbiome and its associations with anal cancer risk factors and clinical factors were analyzed using linear decomposition model and permutational multivariate analysis of variance. Composition of the anal microbiome among HIV positive and high-risk negative women was dominated by Bacteroides, Prevotella, and Campylobacter. The overall taxonomic composition and microbial diversity of the anal microbiome did not significantly differ by HIV status. However, the abundance of Ruminococcus 1 belonging to the Rumincoccaceae family was associated with HIV status (q = .05). No anal cancer risk factors were associated with the anal microbiome composition. Clinical factors marginally associated with the anal microbiome composition included body mass index (BMI; p = .05) and hepatitis C virus (HCV; p = .05). Although HIV and risk factors for anal cancer were not associated with the composition of the anal microbiome in this pilot sample, other clinical factors such as BMI and HCV, may be worth further investigation in a larger study. Future research can build on these findings to explore the role of the microbiome and HIV comorbidities in women.
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Affiliation(s)
- Jessica Wells
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA.,Address correspondence to: Jessica Wells, Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Room 230, Atlanta, GA 30322-1007, USA
| | - Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Despina Tsementzi
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Camber Ileen Jhaney
- Department of Surgery and Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Antonina Foster
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deborah Watkins Bruner
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA.,Department of Surgery and Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Theresa Gillespie
- Department of Surgery and Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Yunxiao Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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22
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Shahi F, Forrester S, Redeker K, Chong JP, Barlow G. Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year. Wellcome Open Res 2022; 7:50. [PMID: 36874581 PMCID: PMC9975432 DOI: 10.12688/wellcomeopenres.17450.1] [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] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global concern and better understanding of the gut microbiome, a known 'amplifier' of AMR, may allow future clinicians to tailor therapy to minimise this risk and offer a personalised medicine approach. To examine the gut microbiome, patients are required to provide faecal samples; more convenient and cheaper solutions need to be found. METHODS As part of a pilot study looking at how routes of administration affect the gut microbiome in NHS patients undergoing routine clinical management for infections, we hypothesised that effects on the gut microbiome varied with the route and metabolism of antibiotic used, and these changes may be reflected in breath metabolites. We present a case report of a patient with an unusual clinical history, alongside breath metabolite and gut microbiome data taken before, during and after antibiotic therapy over a period of one year. RESULTS We noted a shift in the dominant Bacteroides strain in the patient's gut microbiome between pre- and post-therapy samples, along with an alteration in the composition of breath metabolites. CONCLUSIONS This study provides a framework for similar future work and highlights the need for further research on the relationships between changes in microbial gut communities and antimicrobial exposure, patient clinical status, and the metabolites of human breath.
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Affiliation(s)
- Farah Shahi
- Department of Biology, University of York, UK, York, YO10 5DD, UK
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, HU3 2JZ, UK
| | - Sarah Forrester
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - Kelly Redeker
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - James P.J. Chong
- Department of Biology, University of York, UK, York, YO10 5DD, UK
| | - Gavin Barlow
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, HU3 2JZ, UK
- Experimental Medicine and Biomedicine, Hull York Medical School, University of York, York, YO10 5DD, UK
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23
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Shen TCD, Daniel SG, Patel S, Kaplan E, Phung L, Lemelle-Thomas K, Chau L, Herman L, Trisolini C, Stonelake A, Toal E, Khungar V, Bittinger K, Reddy KR, Wu GD. The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis. Gut Microbes 2022; 13:1987781. [PMID: 34747331 PMCID: PMC8583005 DOI: 10.1080/19490976.2021.1987781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Most studies examining correlations between the gut microbiota and disease states focus on fecal samples due to ease of collection, yet there are distinct differences when compared to samples collected from the colonic mucosa. Although fecal microbiota has been reported to be altered in cirrhosis, correlation with mucosal microbiota characterized via rectal swab has not been previously described in this patient population. We conducted a cross-sectional analysis using 39 stool and 39 rectal swabs from adult patients with cirrhosis of different etiologies and performed shotgun metagenomic sequencing. Bacterial growth studies were performed with Escherichia coli. Two asaccharolytic bacterial taxa, Finegoldia magna and Porphyromonas asaccharolytica, were increased in rectal swabs relative to stool (FDR < 0.01). Genomic analysis of the microbiome revealed 58 genes and 16 pathways that differed between stool and rectal swabs (FDR < 0.05), where rectal swabs were enriched for pathways associated with protein synthesis and cellular proliferation but decreased in carbohydrate metabolism. Although no features in the fecal microbiome differentiated cirrhosis etiologies, the mucosal microbiome revealed decreased abundances of E. coli and Enterobacteriaceae in alcohol-related cirrhosis relative to non-alcohol related cirrhosis (FDR < 0.05). In vitro bacterial culture studies showed that physiological concentrations of ethanol and its oxidative metabolites inhibited E. coli growth in a pH- and concentration-dependent manner. Characterization of the mucosally associated gut microbiome via rectal swab revealed findings consistent with amino acid/nitrogen abundance versus carbohydrate limitation in the mucosal microenvironment as well as unique features of alcohol-related cirrhosis possibly consistent with the influence of host-derived metabolites on the composition of mucosally adherent microbiota.
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Affiliation(s)
- Ting-Chin David Shen
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,CONTACT Ting-Chin David Shen 906 BRB II/III, 421 Curie Blvd, Philadelphia, PA19104, USA
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shivali Patel
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily Kaplan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lillian Phung
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kaylin Lemelle-Thomas
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lindsay Herman
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Calvin Trisolini
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aimee Stonelake
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily Toal
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Vandana Khungar
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - K. Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Gary Wu 915 BRB II/III, 421 Curie Blvd, Philadelphia, PA19104, USA
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24
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Chanderraj R, Brown CA, Hinkle K, Falkowski N, Woods RJ, Dickson RP. The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection. MICROBIOME 2022; 10:2. [PMID: 34991717 PMCID: PMC8734160 DOI: 10.1186/s40168-021-01190-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/18/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND In ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for microbiome analysis, yet variation in their bacterial density-and the clinical and methodologic significance of this variation-remains undetermined. We used an ultra-sensitive quantification approach-droplet digital PCR (ddPCR)-to quantify bacterial density in rectal swabs from 118 hospitalized patients. We compared bacterial density with bacterial community composition (via 16S rRNA amplicon sequencing) and clinical data to determine if variation in bacterial density has methodological, clinical, and prognostic significance. RESULTS Bacterial density in rectal swab specimens was highly variable, spanning five orders of magnitude (1.2 × 104-3.2 × 109 16S rRNA gene copies/sample). Low bacterial density was strongly correlated with the detection of sequencing contamination (Spearman ρ = - 0.95, p < 10-16). Low-density rectal swab communities were dominated by peri-rectal skin bacteria and sequencing contaminants (p < 0.01), suggesting that some variation in bacterial density is explained by sampling variation. Yet bacterial density was also associated with important clinical exposures, conditions, and outcomes. Bacterial density was lower among patients who had received piperacillin-tazobactam (p = 0.017) and increased among patients with multiple medical comorbidities (Charlson score, p = 0.0040) and advanced age (p = 0.043). Bacterial density at the time of hospital admission was independently associated with subsequent extraintestinal infection (p = 0.0028), even when controlled for severity of illness and comorbidities. CONCLUSIONS The bacterial density of rectal swabs is highly variable, and this variability is of methodological, clinical, and prognostic significance. Microbiome studies using rectal swabs are vulnerable to sequencing contamination and should include appropriate negative sequencing controls. Among hospitalized patients, gut bacterial density is associated with clinical exposures (antibiotics, comorbidities) and independently predicts infection risk. Bacterial density is an important and under-studied feature of gut microbiome community analysis. Video abstract.
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Affiliation(s)
- Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Weil Institute for Critical Care Research & Innovation, MI, Ann Arbor, USA.
- Pulmonary and Critical Care Medicine, University of Michigan Health System, 6220 MSRB III / SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA.
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25
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The SMML, de Meij TGJ, Budding AE, Bakx R, van der Lee JH, Poort L, Cense HA, Heij HA, van Heurn LWE, Gorter RR. The potential of rectal swabs to differentiate simple and complex appendicitis in children with a microbiota-based test. Eur J Pediatr 2022; 181:4221-4226. [PMID: 36195698 PMCID: PMC9649451 DOI: 10.1007/s00431-022-04627-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/22/2022] [Accepted: 09/12/2022] [Indexed: 11/24/2022]
Abstract
Currently, accurate biomarkers differentiating simple (phlegmonous) from complex (gangrenous and/or perforated) appendicitis in children are lacking. However, both types may potentially require different treatment strategies, and the search for diagnostic modalities remains warranted. Previously, we demonstrated a distinct microbiota (both an increased bacterial diversity and abundance) in the appendix of children with complex compared to simple appendicitis. From the same cohort of patients we have collected 35 rectal swabs under general anesthesia prior to appendectomy and microbiota analysis was performed by IS-pro, a 16S-23S rDNA-based clinical microbiota profiling technique. Using the obtained IS-profiles, we performed cluster analyses (UPGMA), comparison of diversity (Shannon Diversity Index) and intensity (abundance in relative fluorescence units) on phylum level, and comparison on species level of bacteria between simple and complex appendicitis. Regarding these analyses, we observed no clear differences between simple and complex appendicitis. However, increased similarity of the microbial composition of the appendix and rectal swab was found within children with complex compared to simple appendicitis. Furthermore, PLS-DA regression analysis provided clear visual differentiation between simple and complex appendicitis, but the diagnostic power was low (highest AUC 0.65). Conclusion: Microbiota analysis of rectal swabs may be viable to differentiate between simple and complex appendicitis prior to surgery as a supervised classification model allowed for discrimination of both types. However, the current diagnostic power was low and further validation studies are needed to assess the value of this method. What is Known: • Simple and complex appendicitis in children may require different treatment strategies, but accurate preoperative biomarkers are lacking. • Clear differentiation can be made between both types in children based upon the microbial composition in the appendix. What is New: • Increased similarity was found between the microbial composition of the appendix and rectal swab within children with complex compared to simple appendicitis. • Using a supervised classification model rectal swabs may be viable to discriminate between simple and complex appendicitis, but the diagnostic power was low.
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Affiliation(s)
- Sarah-May M. L. The
- grid.414503.70000 0004 0529 2508Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands ,Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Tim G. J. de Meij
- grid.414503.70000 0004 0529 2508Department of Pediatric Gastroenterology, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands ,Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands ,Amsterdam Gastroenterology and Metabolism Research Insititute, Amsterdam, The Netherlands
| | | | - Roel Bakx
- grid.414503.70000 0004 0529 2508Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands ,Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Johanna H. van der Lee
- grid.414503.70000 0004 0529 2508Pediatric Clinical Research Office, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands ,grid.491299.e0000 0004 0448 3177Dutch Knowledge Institute, Federation of Medical Specialists, Utrecht, 3528 BL The Netherlands
| | | | - Huib A. Cense
- grid.415746.50000 0004 0465 7034Department of Surgery, Red Cross Hospital, Beverwijk, 1942 LE The Netherlands
| | - Hugo A. Heij
- grid.414503.70000 0004 0529 2508Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands
| | - L. W. Ernst van Heurn
- grid.414503.70000 0004 0529 2508Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands ,Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands ,Amsterdam Gastroenterology and Metabolism Research Insititute, Amsterdam, The Netherlands
| | - Ramon R. Gorter
- grid.414503.70000 0004 0529 2508Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Centers, location University of Amsterdam, Amsterdam, 1105 AZ The Netherlands ,Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands ,Amsterdam Gastroenterology and Metabolism Research Insititute, Amsterdam, The Netherlands
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26
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Jepsen IE, Saxtorph MH, Englund ALM, Petersen KB, Wissing MLM, Hviid TVF, Macklon N. Probiotic treatment with specific lactobacilli does not improve an unfavorable vaginal microbiota prior to fertility treatment-A randomized, double-blinded, placebo-controlled trial. Front Endocrinol (Lausanne) 2022; 13:1057022. [PMID: 36531460 PMCID: PMC9751370 DOI: 10.3389/fendo.2022.1057022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVE To investigate whether treatment with proprietary lactobacilli-loaded vaginal capsules improves an unfavorable vaginal microbiome diagnosed using a commercially available test and algorithm. DESIGN A randomized, double-blinded, placebo-controlled study was conducted in 74 women prior to undergoing fertility treatment at a single university fertility clinic between April 2019 and February 2021. The women were randomly assigned in a 1:1 ratio to receive one vaginal capsule per day for 10 days containing either a culture of more than 108 CFU of Lactobacillus gasseri and more than 108 CFU Lactobacillus rhamnosus (lactobacilli group) or no active ingredient (placebo group). Vaginal swabs for microbiota analysis were taken at enrollment, after treatment and in the cycle following treatment. PARTICIPANTS AND METHODS Women aged 18-40 years who prior to fertility treatment were diagnosed with an unfavorable vaginal microbiota, characterized by either a low relative load of Lactobacillus or a high proportion of disrupting bacteria using the criteria of the IS-pro™ diagnostic system (ARTPred, Amsterdam, the Netherlands), were enrolled in the study. The primary outcome measure was the proportion of women with improvement of the vaginal microbiota after intervention. RESULTS The vaginal microbiota improved after intervention in 34.2% of all participants (lactobacilli group 28.9%, placebo group 40.0%), with no significant difference in the improvement rate between the lactobacilli and placebo groups, RR = 0.72 (95% CI 0.38-1.38). CONCLUSION This study indicates that administering vaginal probiotics may not be an effective means of modulating the vaginal microbiome for clinical purposes in an infertile population. However, a spontaneous improvement rate of 34.2% over a period of one to three months, confirming the dynamic nature of the vaginal microbiota, indicates that a strategy of postponing further IVF treatment to await microbiota improvement may be relevant in some patients, but further research is needed. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov, identifier NCT03843112.
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Affiliation(s)
- Ida E. Jepsen
- The Fertility Clinic, Department of Obstetrics and Gynecology, Zealand University Hospital, Koege, Denmark
- ReproHealth Research Consortium, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Ida E. Jepsen,
| | - Malene Hviid Saxtorph
- The Fertility Clinic, Department of Obstetrics and Gynecology, Zealand University Hospital, Koege, Denmark
- ReproHealth Research Consortium, Zealand University Hospital, Roskilde, Denmark
| | - Anne Lis Mikkelsen Englund
- The Fertility Clinic, Department of Obstetrics and Gynecology, Zealand University Hospital, Koege, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Thomas Vauvert F. Hviid
- ReproHealth Research Consortium, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Centre for Immune Regulation and Reproductive Immunology, Zealand University Hospital, Roskilde, Denmark
| | - Nicholas Macklon
- The Fertility Clinic, Department of Obstetrics and Gynecology, Zealand University Hospital, Koege, Denmark
- ReproHealth Research Consortium, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- London Women’s Clinic, London, United Kingdom
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27
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Turner G, O’Grady M, Hudson D, Morgan X, Frizelle F, Purcell R. Rectal swabs are a reliable method of assessing the colonic microbiome. Int J Med Microbiol 2022; 312:151549. [DOI: 10.1016/j.ijmm.2022.151549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/11/2022] [Accepted: 01/23/2022] [Indexed: 12/13/2022] Open
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Microbiome Compositions and Resistome Levels after Antibiotic Treatment of Critically Ill Patients: An Observational Cohort Study. Microorganisms 2021; 9:microorganisms9122542. [PMID: 34946144 PMCID: PMC8703874 DOI: 10.3390/microorganisms9122542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/23/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Hospitalization and treatment with antibiotics increase the risk of acquiring multidrug-resistant bacteria due to antibiotic-mediated changes in patient microbiota. This study aimed to investigate how broad- and narrow-spectrum antibiotics affect the gut microbiome and the resistome in antibiotic naïve patients during neurointensive care. Patients admitted to the neurointensive care unit were treated with broad-spectrum (meropenem or piperacillin/tazobactam) or narrow-spectrum antibiotic treatment (including ciprofloxacin, cefuroxime, vancomycin and dicloxacillin) according to clinical indications. A rectal swab was collected from each patient before and after 5–7 days of antibiotic therapy (N = 34), respectively. Shotgun metagenomic sequencing was performed and the composition of metagenomic species (MGS) was determined. The resistome was characterized with CARD RGI software and the CARD database. As a measure for selection pressure in the patient, we used the sum of the number of days with each antibiotic (antibiotic days). We observed a significant increase in richness and a tendency for an increase in the Shannon index after narrow-spectrum treatment. For broad-spectrum treatment the effect was more diverse, with some patients increasing and some decreasing in richness and Shannon index. This was studied further by comparison of patients who had gained or lost >10 MGS, respectively. Selection pressure was significantly higher in patients with decreased richness and a decreased Shannon index who received the broad treatment. A decrease in MGS richness was significantly correlated to the number of drugs administered and the selection pressure in the patient. Bray–Curtis dissimilarities were significant between the pre- and post-treatment of samples in the narrow group, indicating that the longer the narrow-spectrum treatment, the higher the differences between the pre- and the post-treatment microbial composition. We did not find significant differences between pre- and post-treatment for both antibiotic spectrum treatments; however, we observed that most of the antibiotic class resistance genes were higher in abundance in post-treatment after broad-spectrum treatment.
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29
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Kwon YJ, Kwak HJ, Lee HK, Lim HC, Jung DH. Comparison of bacterial community profiles from large intestine specimens, rectal swabs, and stool samples. Appl Microbiol Biotechnol 2021; 105:9273-9284. [PMID: 34773153 DOI: 10.1007/s00253-021-11650-y] [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] [Received: 05/24/2021] [Revised: 10/09/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023]
Abstract
The human gastrointestinal tract contains a complex and dynamic population of microorganisms, known as the gut microbiota. Although interest in the role of the gut microbiota in human health has increased in recent years, there remains no standard sampling protocol for analyzing these organisms. Here, we aimed to characterize the microbial composition of distinct segments of the large intestine and to determine whether rectal swabs are suitable for identifying colon microbiota. A total of 100 participants who underwent screening colonoscopy from October 2019 to October 2020 were included in this study. Large intestinal samples (ascending colon, descending colon, sigmoid colon, and rectum) were aspirated by colonoscopy. Rectal swabs were collected before colonoscopy, and stool samples were collected before patients began colonoscopy preparation. All samples were subjected to 16S ribosomal RNA gene sequencing. We identified differences in the number of phylum-level operational taxonomic units among large intestinal samples, rectal swabs, and stool. Five major phyla were detected in all samples (Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria), although their relative abundances varied. Notably, we found that the microbial compositions of rectal swabs were most similar to those of the sigmoid colon and rectum, whereas the microbiota in stool were relatively different than those from the large intestine and rectal swabs. Our results reveal the existence of microbial heterogeneity within different large intestinal compartments and further suggest that rectal swabs are an acceptable and practical tool for gut microbiota analysis. KEY POINTS: • Our findings highlight local microbiome variations within different regions of the large intestine. • Stool samples do not appear to fully recapitulate the gut microbiome. • Our data from a large population-based cohort indicate that rectal swabs can be used to study the gut microbiome.
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Affiliation(s)
- Yu-Jin Kwon
- Department of Family Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea
| | - Hwan Jong Kwak
- MediCloud Corp, 77, Changnyoung-daero 256beon-gil, Yeongtong-gu, Suwon-si, , Gyeonggi-do, Republic of Korea.,Department of Agriculture and Industry, Kangwon National University, Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Hyung Ki Lee
- MediCloud Corp, 77, Changnyoung-daero 256beon-gil, Yeongtong-gu, Suwon-si, , Gyeonggi-do, Republic of Korea
| | - Hyun Chul Lim
- Department of Gastroenterology, Yongin Severance Hospital, Yonsei University College of Medicine, 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea.
| | - Dong-Hyuk Jung
- Department of Family Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea.
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs. BMC Microbiol 2021; 21:313. [PMID: 34758745 PMCID: PMC8579561 DOI: 10.1186/s12866-021-02374-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02374-0.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK. .,Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.,Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Makhanda (Grahamstown), 6139, South Africa
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Andrew S Brierley
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - David E K Ferrier
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.
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Raimondi S, Candeliere F, Amaretti A, Foschi C, Morselli S, Gaspari V, Rossi M, Marangoni A. Vaginal and Anal Microbiome during Chlamydia trachomatis Infections. Pathogens 2021; 10:1347. [PMID: 34684295 PMCID: PMC8539191 DOI: 10.3390/pathogens10101347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/04/2023] Open
Abstract
Background.Chlamydia trachomatis (CT) is the agent of the most common bacterial sexually transmitted infection worldwide, with a significant impact on women's health. Despite the increasing number of studies about the vaginal microbiome in women with CT infections, information about the composition of the anal microbiome is still lacking. Here, we assessed the bacterial community profiles of vaginal and anal ecosystems associated or not with CT infection in a cohort of Caucasian young women. Methods. A total of 26 women, including 10 with a contemporary vaginal and ano-rectal CT infection, were enrolled. Composition of vaginal and anal microbiome was studied by 16S rRNA gene profiling. Co-occurrence networks of bacterial communities and metagenome metabolic functions were determined. Results. In case of CT infection, both vaginal and anal environments were characterized by a degree of dysbiosis. Indeed, the vaginal microbiome of CT-positive women were depleted in lactobacilli, with a significant increase in dysbiosis-associated bacteria (e.g., Sneathia, Parvimonas, Megasphaera), whereas the anal microbiota of CT-infected women was characterized by higher levels of Parvimonas and Pseudomonas and lower levels of Escherichia. Interestingly, the microbiome of anus and vagina had numerous bacterial taxa in common, reflecting a significant microbial 'sharing' between the two sites. In the vaginal environment, CT positively correlated with Ezakiella spp. while Gardnerella vaginalis co-occurred with several dysbiosis-related microbes, regardless of CT vaginal infection. The vaginal microbiome of CT-positive females exhibited a higher involvement of chorismate and aromatic amino acid biosynthesis, as well as an increase in mixed acid fermentation. Conclusions. These data could be useful to set up new diagnostic/prognostic tools, offering new perspectives for the control of chlamydial infections.
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Affiliation(s)
- Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (S.R.); (F.C.); (A.A.); (M.R.)
| | - Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (S.R.); (F.C.); (A.A.); (M.R.)
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (S.R.); (F.C.); (A.A.); (M.R.)
| | - Claudio Foschi
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy; (S.M.); (A.M.)
| | - Sara Morselli
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy; (S.M.); (A.M.)
| | - Valeria Gaspari
- Dermatology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), St. Orsola Malpighi University Hospital, 40138 Bologna, Italy;
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (S.R.); (F.C.); (A.A.); (M.R.)
| | - Antonella Marangoni
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy; (S.M.); (A.M.)
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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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van Rossen TM, Ooijevaar RE, Kuyvenhoven JP, Eck A, Bril H, Buijsman R, Boermeester MA, Stockmann HBAC, de Korte N, Budding AE. Microbiota composition and mucosal immunity in patients with asymptomatic diverticulosis and controls. PLoS One 2021; 16:e0256657. [PMID: 34492052 PMCID: PMC8423250 DOI: 10.1371/journal.pone.0256657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/11/2021] [Indexed: 01/19/2023] Open
Abstract
INTRODUCTION The etiology of diverticulosis is still poorly understood. However, in patients with diverticulitis, markers of mucosal inflammation and microbiota alterations have been found. The aim of this study was to evaluate potential differences of the gut microbiota composition and mucosal immunity between patients with asymptomatic diverticulosis and controls. METHODS We performed a prospective study on patients who underwent routine colonoscopy for causes not related to diverticular disease or inflammatory bowel disease. Participants were grouped based on the presence or absence of diverticula. Mucosal biopsies were obtained from the sigmoid and transverse colon. Microbiota composition was analyzed with IS-pro, a 16S-23S based bacterial profiling technique. To predict if patients belonged to the asymptomatic diverticulosis or control group a partial least squares discriminant analysis (PLS-DA) regression model was used. Inflammation was assessed by neutrophil and lymphocyte counts within the taken biopsies. RESULTS Forty-three patients were enrolled. Intestinal microbiota profiles were highly similar within individuals for all phyla. Between individuals, microbiota profiles differed substantially but regardless of the presence (n = 19) of absence (n = 24) of diverticula. Microbiota diversity in both sigmoid and transverse colon was similar in all participants. We were not able to differentiate between diverticulosis patients and controls with a PLS-DA model. Mucosal lymphocyte counts were comparable among both groups; no neutrophils were detected in any of the studied biopsies. CONCLUSIONS Microbiota composition and inflammatory markers were comparable among asymptomatic diverticulosis patients and controls. This suggests that the gut microbiota and mucosal inflammation do not play a major role in the pathogenesis of diverticula formation.
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Affiliation(s)
- Tessel M. van Rossen
- Department of Medical Microbiology & Infection Control, Amsterdam Institute for Infection & Immunity, Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| | - Rogier E. Ooijevaar
- Department of Gastroenterology & Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Johan Ph. Kuyvenhoven
- Department of Gastroenterology & Hepatology, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Anat Eck
- Department of Medical Microbiology & Infection Control, Amsterdam Institute for Infection & Immunity, Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Herman Bril
- Department of Pathology, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - René Buijsman
- Department of Traumasurgery, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Marja A. Boermeester
- Department of Surgery, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Niels de Korte
- Department of Surgery, Spaarne Gasthuis, Hoofddorp, The Netherlands
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Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies. mSystems 2021; 6:e0075021. [PMID: 34427527 PMCID: PMC8407471 DOI: 10.1128/msystems.00750-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The advent of high-throughput sequencing techniques has recently provided an astonishing insight into the composition and function of the human microbiome. Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. Despite the wide availability and the enormous potential for clinical and translational applications, ONT is poorly standardized in terms of sampling and storage conditions, DNA extraction, library creation, and bioinformatic classification. Here, we present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatic evaluation for complex microbiomes sequenced with ONT. Our findings from buccal and rectal swabs and DNA extraction experiments indicate that methods that were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Our benchmarking experiments reveal thresholds for analysis parameters that achieved excellent precision, recall, and area under the precision recall values and is superior to existing classifiers (Kraken2, Kaiju, and MetaMaps). Hence, our workflow provides an experimental and bioinformatic pipeline to perform a highly accurate analysis of complex microbial structures from buccal and rectal swabs. IMPORTANCE Advanced microbiome analysis relies on sequencing of short DNA fragments from microorganisms like bacteria, fungi, and viruses. More recently, long fragment DNA sequencing of 3rd generation sequencing has gained increasing importance and can be rapidly conducted within a few hours due to its potential real-time sequencing. However, the analysis and correct identification of the microbiome relies on a multitude of factors, such as the method of sampling, DNA extraction, sequencing, and bioinformatic analysis. Scientists have used different protocols in the past that do not allow us to compare results across different studies and research fields. Here, we provide a comprehensive workflow from DNA extraction, sequencing, and bioinformatic workflow that allows rapid and accurate analysis of human buccal and rectal swabs with reproducible protocols. This workflow can be readily applied by many scientists from various research fields that aim to use long-fragment microbiome sequencing.
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Ammer-Herrmenau C, Asendorf T, Beyer G, Buchholz SM, Cameron S, Damm M, Frost F, Henker R, Jaster R, Phillip V, Placzek M, Ratei C, Sirtl S, van den Berg T, Weingarten MJ, Woitalla J, Mayerle J, Ellenrieder V, Neesse A. Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis-a prospective multicentre translational study. BMC Gastroenterol 2021; 21:304. [PMID: 34332533 PMCID: PMC8325304 DOI: 10.1186/s12876-021-01885-4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Background Acute pancreatitis (AP) is an inflammatory disorder that causes a considerable economic health burden. While the overall mortality is low, around 20% of patients have a complicated course of disease resulting in increased morbidity and mortality. There is an emerging body of evidence that the microbiome exerts a crucial impact on the pathophysiology and course of AP. For several decades multiple clinical and laboratory parameters have been evaluated, and complex scoring systems were developed to predict the clinical course of AP upon admission. However, the majority of scoring systems are determined after several days and achieve a sensitivity around 70% for early prediction of severe AP. Thus, continued efforts are required to investigate reliable biomarkers for the early prediction of severity in order to guide early clinical management of AP patients.
Methods We designed a multi-center, prospective clinical-translational study to test whether the orointestinal microbiome may serve as novel early predictor of the course, severity and outcome of patients with AP. We will recruit 400 AP patients and obtain buccal and rectal swabs within 72 h of admission to the hospital. Following DNA extraction, microbiome analysis will be performed using 3rd generation sequencing Oxford Nanopore Technologies (ONT) for 16S rRNA and metagenomic sequencing. Alpha- and beta-diversity will be determined and correlated to the revised Atlanta classification and additional clinical outcome parameters such as the length of hospital stay, number and type of complications, number of interventions and 30-day mortality. Discussion If AP patients show a distinct orointestinal microbiome dependent on the severity and course of the disease, microbiome sequencing could rapidly be implemented in the early clinical management of AP patients in the future. Trial registration: ClinicalTrials.gov Identifier: NCT04777812
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Affiliation(s)
- C Ammer-Herrmenau
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - T Asendorf
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - G Beyer
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - S M Buchholz
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - S Cameron
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - M Damm
- Department of Medicine I, University Hospital Halle, Halle, Germany
| | - F Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - R Henker
- Division of Gastroenterology, Medical Department II, University Hospital of Leipzig, Leipzig, Germany
| | - R Jaster
- Department of Medicine II, University Hospital Rostock, Rostock, Germany
| | - V Phillip
- Department of Medicine II, University Hospital rechts der Isar, Technical University Munich, Munich, Germany
| | - M Placzek
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - C Ratei
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - S Sirtl
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - T van den Berg
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - M J Weingarten
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - J Woitalla
- Department of Medicine II, University Hospital Rostock, Rostock, Germany
| | - J Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - V Ellenrieder
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - A Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany.
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Perler BK, Reinhart EM, Montgomery M, Maynard M, Shapiro JM, Belenky P, Chan PA. Evaluation of the Microbiome in Men Taking Pre-exposure Prophylaxis for HIV Prevention. AIDS Behav 2021; 25:2005-2013. [PMID: 33394167 DOI: 10.1007/s10461-020-03130-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 01/04/2023]
Abstract
Tenofovir-based regimens as pre-exposure prophylaxis (PrEP) are highly effective at preventing HIV infection. The most common side-effect is gastrointestinal (GI) distress which may be associated with changes in the microbiome. Dysbiosis of the microbiome can have numerous health-related consequences. To understand the effect of PrEP on dysbiosis, we evaluated 27 individuals; 14 were taking PrEP for an average of 171 weeks. Sequencing of 16S rRNA was performed using self-collected rectal swabs. Mixed beta diversity testing demonstrated significant differences between PrEP and non-PrEP users with Bray-Curtis and unweighted UniFrac analyses (p = 0.05 and 0.049, respectively). At the genus level, there was a significant reduction in Finegoldia, along with a significant increase in Catenibacterium and Prevotella in PrEP users. Prevotella has been associated with inflammatory pathways, insulin resistance and cardiovascular disease, while Catenibacterium has been associated with morbid obesity and metabolic syndrome. Overall, these results suggest that PrEP may be associated with some degree of microbiome dysbiosis, which may contribute to GI symptoms. Long-term impact of these changes is unknown.
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Auguet OT, Niehus R, Gweon HS, Berkley JA, Waichungo J, Njim T, Edgeworth JD, Batra R, Chau K, Swann J, Walker SA, Peto TE, Crook DW, Lamble S, Turner P, Cooper BS, Stoesser N. Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. EClinicalMedicine 2021; 36:100910. [PMID: 34124634 PMCID: PMC8173267 DOI: 10.1016/j.eclinm.2021.100910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) in Enterobacterales is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines. METHODS In this exploratory study, a novel approach to population-level prediction of AMR in Enterobacterales clinical isolates using metagenomic (Illumina) profiling of pooled DNA extracts from human faecal samples was developed and tested. Taxonomic and AMR gene profiles were used to derive taxonomy-adjusted population-level AMR metrics. Bayesian modelling, and model comparison based on cross-validation, were used to evaluate the capacity of each metric to predict the number of resistant Enterobacterales invasive infections at a population-level, using available bloodstream/cerebrospinal fluid infection data. FINDINGS Population metagenomes comprised samples from 177, 157, and 156 individuals in Kenya, the UK, and Cambodia, respectively, collected between September 2014 and April 2016. Clinical data from independent populations included 910, 3356 and 197 bacterial isolates from blood/cerebrospinal fluid infections in Kenya, the UK and Cambodia, respectively (samples collected between January 2010 and May 2017). Enterobacterales were common colonisers and pathogens, and faecal taxonomic/AMR gene distributions and proportions of antimicrobial-resistant Enterobacterales infections differed by setting. A model including terms reflecting the metagenomic abundance of the commonest clinical Enterobacterales species, and of AMR genes known to either increase the minimum inhibitory concentration (MIC) or confer clinically-relevant resistance, had a higher predictive performance in determining population-level resistance in clinical Enterobacterales isolates compared to models considering only AMR gene information, only taxonomic information, or an intercept-only baseline model (difference in expected log predictive density compared to best model, estimated using leave-one-out cross-validation: intercept-only model = -223 [95% credible interval (CI): -330,-116]; model considering only AMR gene information = -186 [95% CI: -281,-91]; model considering only taxonomic information = -151 [95% CI: -232,-69]). INTERPRETATION Whilst our findings are exploratory and require validation, intermittent metagenomics of pooled samples could represent an effective approach for AMR surveillance and to predict population-level AMR in clinical isolates, complementary to ongoing development of laboratory infrastructures processing individual samples.
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Affiliation(s)
- Olga Tosas Auguet
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Rene Niehus
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Hyun Soon Gweon
- School of Biological Sciences, University of Reading, Reading, UK
- Centre for Ecology & Hydrology, Wallingford, UK
| | - James A. Berkley
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
| | | | - Tsi Njim
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Jonathan D. Edgeworth
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London, London, UK
| | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah A. Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Tim E.A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia-Oxford Medical Research Unit, Microbiology Department, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ben S. Cooper
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
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Summers SC, Galloni A, Webb CB. Impact of specimen type on findings for bacterial composition within the intestinal tract of dogs and cats with and without chronic enteropathy. Am J Vet Res 2021; 82:494-501. [PMID: 34032481 DOI: 10.2460/ajvr.82.6.494] [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: 11/20/2022]
Abstract
OBJECTIVE To compare bacterial diversity and community composition among fecal, rectal swab, and colonic mucosal biopsy specimens from dogs and cats with and without chronic enteropathy (CE). ANIMALS 9 healthy dogs, 8 dogs with CE, 8 healthy cats, and 9 cats with CE. PROCEDURES In a cross-sectional study design, fecal, rectal swab, and colonic mucosal biopsy specimens were obtained by colonoscopy from healthy dogs and dogs and cats with CE. Fecal and rectal swab specimens were collected from healthy cats. Genomic DNA was extracted, the 16S rRNA V4 gene region was amplified, and sequencing was performed by use of primers 515F to 806R on a paired-end platform. RESULTS For healthy dogs and dogs and cats with CE, bacterial diversity based on the Chao1 estimate of total species richness was higher for colonic mucosal biopsy specimens than for fecal specimens. Analysis of similarities by use of the Bray-Curtis dissimilarity index revealed that the bacterial communities captured in rectal swab specimens were similar to those captured in fecal specimens for healthy dogs and dogs with CE and similar to those captured in colonic mucosal biopsy specimens for both dog groups and cats with CE. CONCLUSIONS AND CLINICAL RELEVANCE Rectal swab and colonic biopsy specimens were successfully used to characterize the bacteriome of the intestinal tract in dogs and cats by 16S rRNA gene sequencing. Although the specimen types evaluated in this study were not interchangeable in results, rectal swab specimens were practical to collect from dogs and cats to study bacterial composition within the intestinal tract and may provide an alternative to colonic mucosal biopsy and fecal specimens.
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Janiak MC, Montague MJ, Villamil CI, Stock MK, Trujillo AE, DePasquale AN, Orkin JD, Bauman Surratt SE, Gonzalez O, Platt ML, Martínez MI, Antón SC, Dominguez-Bello MG, Melin AD, Higham JP. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques. MICROBIOME 2021; 9:68. [PMID: 33752735 PMCID: PMC7986251 DOI: 10.1186/s40168-021-01009-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada.
- Alberta Children's Hospital Research Institute, Alberta, Canada.
- Department of Anthropology, New York University, New York, USA.
- School of Science, Engineering and Environment, University of Salford, Salford, UK.
| | - Michael J Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Catalina I Villamil
- School of Chiropractic, Universidad Central del Caribe, Bayamón, Puerto Rico
| | - Michala K Stock
- Department of Sociology and Anthropology, Metropolitan State University of Denver, Denver, CO, USA
| | - Amber E Trujillo
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Allegra N DePasquale
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - Olga Gonzalez
- Disease Intervention and Prevention, Southwest National Primate Research Center, San Antonio, TX, USA
| | - Michael L Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Susan C Antón
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Alberta, Canada
| | - James P Higham
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
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Short MI, Hudson R, Besasie BD, Reveles KR, Shah DP, Nicholson S, Johnson-Pais TL, Weldon K, Lai Z, Leach RJ, Fongang B, Liss MA. Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling. BMC Microbiol 2021; 21:26. [PMID: 33446094 PMCID: PMC7809826 DOI: 10.1186/s12866-020-02080-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/22/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a timely manner so as not to alter the microbial content. Due to the logistical difficulties of home-based stool collection, there has been a challenge in selecting the appropriate sample collection technique and comparing results from different microbiome studies. Thus, we compared stool collection and two alternative clinic-based fecal microbiome collection techniques, including a newer glove-based collection method. RESULTS We prospectively enrolled 22 adult men from our prostate cancer screening cohort SABOR (San Antonio Biomarkers of Risk for prostate cancer) in San Antonio, TX, from 8/2018 to 4/2019. A rectal swab and glove tip sample were collected from each participant during a one-time visit to our clinics. A single stool sample was collected at the participant's home. DNA was isolated from the fecal material and 16 s rRNA sequencing of the V1-V2 and V3-V4 regions was performed. We found the gut microbiome to be similar in richness and evenness, noting no differences in alpha diversity among the collection methods. The stool collection method, which remains the gold-standard method for the gut microbiome, proved to have different community composition compared to swab and glove tip techniques (p< 0.001) as measured by Bray-Curtis and unifrac distances. There were no significant differences in between the swab and glove tip samples with regard to beta diversity (p> 0.05). Despite differences between home-based stool and office-based fecal collection methods, we noted that the distance metrics for the three methods cluster by participant indicating within-person similarities. Additionally, no taxa differed among the methods in a Linear Discriminant Analysis Effect Size (LEfSe) analysis comparing all-against-all sampling methods. CONCLUSION The glove tip method provides similar gut microbiome results as rectal swab and stool microbiome collection techniques. The addition of a new office-based collection technique could help easy and practical implementation of gut microbiome research studies and clinical practice.
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Affiliation(s)
- Meghan I Short
- University of Texas Health San Antonio, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
| | - Robert Hudson
- Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Benjamin D Besasie
- Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Kelly R Reveles
- The University of Texas at Austin, College of Pharmacy, Austin, TX, USA
| | - Dimpy P Shah
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Susannah Nicholson
- Department of Surgery, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Teresa L Johnson-Pais
- Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Korri Weldon
- University of Texas Health San Antonio, Genome Sequencing Facility, Greehey Children's Cancer Research Institute (GCCRI), San Antonio, TX, USA
| | - Zhao Lai
- University of Texas Health San Antonio, Genome Sequencing Facility, Greehey Children's Cancer Research Institute (GCCRI), San Antonio, TX, USA
| | - Robin J Leach
- Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Bernard Fongang
- University of Texas Health San Antonio, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Michael A Liss
- Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
- The University of Texas at Austin, College of Pharmacy, Austin, TX, USA.
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Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India. mSphere 2020; 5:5/5/e00731-20. [PMID: 32968008 PMCID: PMC7568645 DOI: 10.1128/msphere.00731-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this cross-sectional study, we describe the composition and diversity of the gut microbiota among undernourished children living in urban slums of Mumbai, India, and determine how nutritional status, including anthropometric measurements, dietary intakes from complementary foods, feeding practices, and micronutrient concentrations, is associated with their gut microbiota. We collected rectal swabs from children aged 10 to 18 months living in urban slums of Mumbai participating in a randomized controlled feeding trial and conducted 16S rRNA sequencing to determine the composition of the gut microbiota. Across the study cohort, Proteobacteria dominated the gut microbiota at over 80% relative abundance, with Actinobacteria representation at <4%, suggesting immaturity of the gut. Increased microbial α-diversity was associated with current breastfeeding, greater head circumference, higher fat intake, and lower hemoglobin concentration and weight-for-length Z-score. In redundancy analyses, 47% of the variation in Faith's phylogenetic diversity (Faith's PD) could be accounted for by age and by iron and polyunsaturated fatty acid intakes. Differences in community structure (β-diversity) of the microbiota were observed among those consuming fats and oils the previous day compared to those not consuming fats and oils the previous day. Our findings suggest that growth, diet, and feeding practices are associated with gut microbiota metrics in undernourished children, whose gut microbiota were comprised mainly of Proteobacteria, a phylum containing many potentially pathogenic taxa.IMPORTANCE The impact of comprehensive nutritional status, defined as growth, nutritional blood biomarkers, dietary intakes, and feeding practices, on the gut microbiome in children living in low-resource settings has remained underreported in microbiome research. Among undernourished children living in urban slums of Mumbai, India, we observed a high relative abundance of Proteobacteria, a phylum including many potentially pathogenic species similar to the composition in preterm infants, suggesting immaturity of the gut, or potentially a high inflammatory burden. We found head circumference, fat and iron intake, and current breastfeeding were positively associated with microbial diversity, while hemoglobin and weight for length were associated with lower diversity. Findings suggest that examining comprehensive nutrition is critical to gain more understanding of how nutrition and the gut microbiota are linked, particularly in vulnerable populations such as children in urban slum settings.
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Faucher MA, Greathouse KL, Hastings-Tolsma M, Padgett RN, Sakovich K, Choudhury A, Sheikh A, Ajami NJ, Petrosino JF. Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study. Am J Perinatol 2020; 37:1160-1172. [PMID: 31242511 DOI: 10.1055/s-0039-1692715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE This study determines the differences in the distal gut and vaginal microbiome in African American (AA) women by prepregnancy body mass index and gestational weight gain (GWG) comparing women with and without obesity and by obesity class. STUDY DESIGN We prospectively sampled the vaginal and distal gut microbiome in pregnant AA women at two time points during pregnancy. Samples were analyzed using high-throughput sequencing of the V4 region of the 16S ribosomal ribonucleic acid gene. RESULTS Distinct differences in vaginal and distal gut α-diversity were observed at time point 1 between women with and without obesity by total GWG. Significant differences in distal gut β-diversity were also found at time point 1 in obese women by GWG. Within the Bacteroides genus, a significant association was observed by total GWG among obese women which was absent in nonobese women. Women with class III obesity who experienced low GWG had the lowest abundance of distal gut Bacteroides and appreciably higher relative abundance of a consortia of vaginal taxa including Atopobium, Gardnerella, Prevotella, and Sneathia. CONCLUSION These results contribute new evidence showing that GWG in combination with obesity and obesity class is associated with an altered distal gut and vaginal composition early in pregnancy among AA women.
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Affiliation(s)
- Mary Ann Faucher
- Louise Herrington School of Nursing, Midwifery Specialty, Baylor University, Dallas, Texas
| | | | - Marie Hastings-Tolsma
- Louise Herrington School of Nursing, Midwifery Specialty, Baylor University, Dallas, Texas
| | | | - Kimberly Sakovich
- Women's Health Care, MacArthur Obstetrics and Gynecology, Irving, Texas
| | | | - Aadil Sheikh
- Department of Biology, Baylor University, Waco, Texas
| | - Nadim J Ajami
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Texas Medical Center, Houston, Texas
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Texas Medical Center, Houston, Texas
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Maasch JRMA, Arzika AM, Cook C, Lebas E, Pilotte N, Grant JR, Williams SA, Keenan JD, Lietman TM, Aiemjoy K. Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis. Am J Trop Med Hyg 2020; 103:1276-1282. [PMID: 32524959 PMCID: PMC7470573 DOI: 10.4269/ajtmh.19-0909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/02/2020] [Indexed: 12/19/2022] Open
Abstract
Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Paired rectal swab and bulk stool samples were collected from 86 children ages 0-4 years living in southwest Niger, with duplicate samples collected among a subset of 50 children. Infection was detected using a previously validated real-time PCR diagnostic targeting the small subunit ribosomal RNA gene. Giardia duodenalis was detected in 65.5% (55/84) of bulk stool samples and 44.0% (37/84) of swab samples. The kappa evaluating test agreement was 0.81 (95% CI: 0.54-1.00) among duplicate stool samples (N = 49) and 0.75 (95% CI: 0.47-1.00) among duplicate rectal swabs (N = 48). Diagnostic sensitivity was 93% (95% CI: 84-98) by bulk stool and 63% (95% CI: 49-75) by rectal swabs. When restricting to the lowest three quartiles of bulk stool quantitation cycle values (an indication of relatively high parasite load), sensitivity by rectal swabs increased to 78.0% (95% CI: 64-89, P < 0.0001). These findings suggest that rectal swabs provide less sensitive and reproducible results than bulk stool for the real-time PCR diagnosis of G. duodenalis. However, their fair sensitivity for higher parasite loads suggests that swabs may be a useful tool for detecting higher burden infections when stool collection is excessively expensive or logistically challenging.
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Affiliation(s)
| | | | - Catherine Cook
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Elodie Lebas
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts
| | - Jessica R. Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts
| | - Jeremy D. Keenan
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Thomas M. Lietman
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Kristen Aiemjoy
- Proctor Foundation, University of California San Francisco, San Francisco, California
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
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Munck C, Sheth RU, Cuaresma E, Weidler J, Stump SL, Zachariah P, Chong DH, Uhlemann AC, Abrams JA, Wang HH, Freedberg DE. The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study. Crit Care 2020; 24:404. [PMID: 32646458 PMCID: PMC7350675 DOI: 10.1186/s13054-020-03061-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The need for early antibiotics in the intensive care unit (ICU) is often balanced against the goal of antibiotic stewardship. Long-course antibiotics increase the burden of antimicrobial resistance within colonizing gut bacteria, but the dynamics of this process are not fully understood. We sought to determine how short-course antibiotics affect the antimicrobial resistance phenotype and genotype of colonizing gut bacteria in the ICU by performing a prospective cohort study with assessments of resistance at ICU admission and exactly 72 h later. METHODS Deep rectal swabs were performed on 48 adults at the time of ICU admission and exactly 72 h later, including patients who did and did not receive antibiotics. To determine resistance phenotype, rectal swabs were cultured for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). In addition, Gram-negative bacterial isolates were cultured against relevant antibiotics. To determine resistance genotype, quantitative PCR (qPCR) was performed from rectal swabs for 87 established resistance genes. Within-individual changes in antimicrobial resistance were calculated based on culture and qPCR results and correlated with exposure to relevant antibiotics (e.g., did β-lactam antibiotic exposure associate with a detectable change in β-lactam resistance over this 72-h period?). RESULTS Of 48 ICU patients, 41 (85%) received antibiotics. Overall, there was no increase in the antimicrobial resistance profile of colonizing gut bacteria during the 72-h study period. There was also no increase in antimicrobial resistance after stratification by receipt of antibiotics (i.e., no detectable increase in β-lactam, vancomycin, or macrolide resistance regardless of whether patients received those same antibiotics). This was true for both culture and PCR. Antimicrobial resistance pattern at ICU admission strongly predicted resistance pattern after 72 h. CONCLUSIONS Short-course ICU antibiotics made little detectable difference in the antimicrobial resistance pattern of colonizing gut bacteria over 72 h in the ICU. This provides an improved understanding of the dynamics of antimicrobial resistance in the ICU and some reassurance that short-course antibiotics may not adversely impact the stewardship goal of reducing antimicrobial resistance.
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Affiliation(s)
- Christian Munck
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA.
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Edward Cuaresma
- Department of Medicine, Columbia University Irving Medical Center, New York, USA
| | - Jessica Weidler
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Stephania L Stump
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Philip Zachariah
- Division of Pediatric Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - David H Chong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA.
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Shogan BD, Chen J, Duchalais E, Collins D, Chang M, Krull K, Krezalek MA, Larson DW, Walther-Antonio MR, Chia N, Nelson H. Alterations of the Rectal Microbiome Are Associated with the Development of Postoperative Ileus in Patients Undergoing Colorectal Surgery. J Gastrointest Surg 2020; 24:1663-1672. [PMID: 32323252 DOI: 10.1007/s11605-020-04593-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/02/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND The most common complications after colorectal surgery, postoperative ileus, surgical site infections, and anastomotic leaks continue to occur despite advances in surgical technique and enhanced recovery pathways. Preclinical studies have documented that intestinal bacteria play a role in the development of these complication, yet human data is lacking. Here we hypothesized that patients that develop ileus, surgical site infection, and/or anastomotic leak following colorectal surgery harbor a specific preoperative gut microbiome. METHODS We performed a prospective cohort study on 101 patients undergoing colon or rectal resection at the Mayo Clinic. Rectal samples were collected preoperatively and on the ward on postoperative day two. The bacterial community from each sample was characterized by 16S rRNA and associated with the development of complications. RESULTS The rectal microbiome collected from patients in the operating room (p = .003) and on postoperative day two (p = .001) was significantly difference in patients whom later developed postoperative ileus compared with patients that had a normal return of bowel function. Patients whom developed ileus showed increased abundance of Bacteroides spp., Parabacteroides spp., and Ruminococcus spp., bacteria that are associated with promoting intestinal inflammation. There were no differences in the microbiome in patients that developed surgical site infections or anastomotic leaks. CONCLUSIONS In this pilot study, patients that develop postoperative ileus harbor a specific gut microbiome during the perioperative period. These findings demonstrate that the preoperative bacterial composition may predispose patients to the development of ileus and that perioperative manipulation of the gut bacteria may provide a novel method to promote normal return of bowel function.
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Affiliation(s)
- Benjamin D Shogan
- Division of Colon and Rectal Surgery, University of Chicago, Room J557F, MC 5095, 5841 S. Maryland Ave, Chicago, IL, 60637, USA.
| | - Jun Chen
- Division of Biomedical Statistics, Mayo Clinic, Rochester, MN, USA
| | - Emilie Duchalais
- Department of Digestive and Endocrine Surgery, CHU de Nantes, Nantes, France
| | | | - Melissa Chang
- Department of Surgery, St. Joseph Mercy Hospital, Ann Arbor, MI, USA
| | - Kimberly Krull
- Division of Colon and Rectal Surgery, Mayo Clinic, Rochester, MN, USA
| | - Monika A Krezalek
- Division of Colon and Rectal Surgery, Mayo Clinic, Rochester, MN, USA
| | - David W Larson
- Division of Colon and Rectal Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Nicholas Chia
- Division of Biomedical Statistics, Mayo Clinic, Rochester, MN, USA
| | - Heidi Nelson
- Division of Colon and Rectal Surgery, Mayo Clinic, Rochester, MN, USA
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A prospective study in severely injured patients reveals an altered gut microbiome is associated with transfusion volume. J Trauma Acute Care Surg 2020; 86:573-582. [PMID: 30633104 PMCID: PMC6433524 DOI: 10.1097/ta.0000000000002201] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Traumatic injury can lead to a compromised intestinal epithelial barrier and inflammation. While alterations in the gut microbiome of critically injured patients may influence clinical outcomes, the impact of trauma on gut microbial composition is unknown. Our objective was to determine if the gut microbiome is altered in severely injured patients and begin to characterize changes in the gut microbiome due to time and therapeutic intervention. METHODS We conducted a prospective, observational study in adult patients (n = 72) sustaining severe injury admitted to a Level I Trauma Center. Healthy volunteers (n = 13) were also examined. Fecal specimens were collected on admission to the emergency department and at 3, 7, 10, and 13 days (±2 days) following injury. Microbial DNA was isolated for 16s rRNA sequencing, and α and β diversities were estimated, according to taxonomic classification against the Greengenes database. RESULTS The gut microbiome of trauma patients was altered on admission (i.e., within 30 minutes following injury) compared to healthy volunteers. Patients with an unchanged gut microbiome on admission were transfused more RBCs than those with an altered gut microbiome (p < 0.001). Although the gut microbiome started to return to a β-diversity profile similar to that of healthy volunteers over time, it remained different from healthy controls. Alternatively, α diversity initially increased postinjury, but subsequently decreased during the hospitalization. Injured patients on admission had a decreased abundance of traditionally beneficial microbial phyla (e.g., Firmicutes) with a concomitant decrease in opportunistic phyla (e.g., Proteobacteria) compared to healthy controls (p < 0.05). Large amounts of blood products and RBCs were both associated with higher α diversity (p < 0.001) and a β diversity clustering closer to healthy controls. CONCLUSION The human gut microbiome changes early after trauma and may be aided by early massive transfusion. Ultimately, the gut microbiome of trauma patients may provide valuable diagnostic and therapeutic insight for the improvement of outcomes postinjury. LEVEL OF EVIDENCE Prognostic and Epidemiological, level III.
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Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue. mSystems 2020; 5:5/2/e00138-20. [PMID: 32291348 PMCID: PMC7159898 DOI: 10.1128/msystems.00138-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes. As research focusing on the colorectal cancer fecal microbiome using shotgun sequencing continues, increasing evidence has supported correlations between colorectal carcinomas (CRCs) and fecal microbiome dysbiosis. However, large-scale on-site and off-site (surrounding adjacent) tissue microbiome characterization of CRC was underrepresented. Here, considering each taxon as a feature, we demonstrate a machine learning-based method to investigate tissue microbial differences among CRC, colorectal adenoma (CRA), and healthy control groups using 16S rRNA data sets retrieved from 15 studies. A total of 2,099 samples were included and analyzed in case-control comparisons. Multiple methods, including differential abundance analysis, random forest classification, cooccurrence network analysis, and Dirichlet multinomial mixture analysis, were conducted to investigate the microbial signatures. We showed that the dysbiosis of the off-site tissue of colonic cancer was distinctive and predictive. The AUCs (areas under the curve) were 80.7%, 96.0%, and 95.8% for CRC versus healthy control random forest models using stool, tissue, and adjacent tissue samples and 69.9%, 91.5%, and 89.5% for the corresponding CRA models, respectively. We also found that the microbiota ecologies of the surrounding adjacent tissues of CRC and CRA were similar to their on-site counterparts according to network analysis. Furthermore, based on the enterotyping of tissue samples, the cohort-specific microbial signature might be the crux in addressing classification generalization problems. Despite cohort heterogeneity, the dysbiosis of lesion-adjacent tissues might provide us with further perspectives in demonstrating the role of the microbiota in colorectal cancer tumorigenesis. IMPORTANCE Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes.
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Rowan-Nash AD, Araos R, D'Agata EMC, Belenky P. Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts. iScience 2020; 23:100905. [PMID: 32106056 PMCID: PMC7044522 DOI: 10.1016/j.isci.2020.100905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/10/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Long-term care facilities are significant reservoirs of antimicrobial-resistant organisms, and patients with advanced dementia are particularly vulnerable to multidrug-resistant organism (MDRO) acquisition and antimicrobial overuse. In this study, we longitudinally examined a group of patients with advanced dementia using metagenomic sequencing. We found significant inter- and intra-subject heterogeneity in microbiota composition, suggesting temporal instability. We also observed a link between the antimicrobial resistance gene density in a sample and the relative abundances of several pathobionts, particularly Escherichia coli, Proteus mirabilis, and Enterococcus faecalis, and used this relationship to predict resistance gene density in samples from additional subjects. Furthermore, we used metagenomic assembly to demonstrate that these pathobionts had higher resistance gene content than many gut commensals. Given the frequency and abundances at which these pathobionts were found in this population and the underlying vulnerability to MDRO of patients with advanced dementia, attention to microbial blooms of these species may be warranted.
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Affiliation(s)
- Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Rafael Araos
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile; Millenium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile; Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Erika M C D'Agata
- Infectious Diseases Division, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
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Aardema H, Lisotto P, Kurilshikov A, Diepeveen JRJ, Friedrich AW, Sinha B, de Smet AMGA, Harmsen HJM. Marked Changes in Gut Microbiota in Cardio-Surgical Intensive Care Patients: A Longitudinal Cohort Study. Front Cell Infect Microbiol 2020; 9:467. [PMID: 32010644 PMCID: PMC6974539 DOI: 10.3389/fcimb.2019.00467] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Virtually no studies on the dynamics of the intestinal microbiota in patients admitted to the intensive care unit (ICU) are published, despite the increasingly recognized important role of microbiota on human physiology. Critical care patients undergo treatments that are known to influence the microbiota. However, dynamics and extent of such changes are not yet fully understood. To address this topic, we analyzed the microbiota before, during and after planned major cardio surgery that, for the first time, allowed us to follow the microbial dynamics of critical care patients. In this prospective, observational, longitudinal, single center study, we analyzed the fecal microbiota using 16S rRNA gene sequencing. Results: Samples of 97 patients admitted between April 2015 and November 2016 were included. In 32 patients, data of all three time points (before, during and after admission) were available for analysis. We found a large intra-individual variation in composition of gut microbiota. During admission, a significant change in microbial composition occurred in most patients, with a significant increase in pathobionts combined with a decrease in strictly anaerobic gut bacteria, typically beneficial for health. A lower bacterial diversity during admission was associated with longer hospitalization. In most patients analyzed at all three time points, the change in microbiota during hospital stay reverted to the original composition post-discharge. Conclusions: Our study shows that, even with a short ICU stay, patients present a significant change in microbial composition shortly after admission. The unique longitudinal setup of this study displayed a restoration of the microbiota in most patients to baseline composition post-discharge, which demonstrated its great restorative capacity. A relative decrease in benign or even beneficial bacteria and increase of pathobionts shifts the microbial balance in the gut, which could have clinical relevance. In future studies, the microbiota of ICU patients should be considered a good target for optimisation.
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Affiliation(s)
- Heleen Aardema
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paola Lisotto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Janneke R J Diepeveen
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anne Marie G A de Smet
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Marques FZ, Jama HA, Tsyganov K, Gill PA, Rhys-Jones D, Muralitharan RR, Muir J, Holmes A, Mackay CR. Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension. Hypertension 2019; 74:1279-1293. [DOI: 10.1161/hypertensionaha.119.13079] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hypertension is a complex and modifiable condition in which environmental factors contribute to both onset and progression. Recent evidence has accumulated for roles of diet and the gut microbiome as environmental factors in blood pressure regulation. However, this is complex because gut microbiomes are a unique feature of each individual reflecting that individual’s developmental and environmental history creating caveats for both experimental models and human studies. Here, we describe guidelines for conducting gut microbiome studies in experimental and clinical hypertension. We provide a complete guide for authors on proper design, analyses, and reporting of gut microbiota/microbiome and metabolite studies and checklists that can be used by reviewers and editors to support robust reporting and interpretation. We discuss factors that modulate the gut microbiota in animal (eg, cohort, controls, diet, developmental age, housing, sex, and models used) and human studies (eg, blood pressure measurement and medication, body mass index, demographic characteristics including age, cultural identification, living structure, sex and socioeconomic environment, and exclusion criteria). We also provide best practice advice on sampling, storage of fecal/cecal samples, DNA extraction, sequencing methods (including metagenomics and 16S rRNA), and computational analyses. Finally, we discuss the measurement of short-chain fatty acids, metabolites produced by the gut microbiota, and interpretation of data. These guidelines should support better transparency, reproducibility, and translation of findings in the field of gut microbiota/microbiome in hypertension and cardiovascular disease.
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Affiliation(s)
- Francine Z. Marques
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Australia (F.Z.M., H.A.J.)
| | - Hamdi A. Jama
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Australia (F.Z.M., H.A.J.)
| | - Kirill Tsyganov
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
| | - Paul A. Gill
- Translational Nutrition Science in the Department of Gastroenterology, Central Clinical School (P.A.G., J.M., D.R-J.), Monash University, Melbourne, Australia
| | - Dakota Rhys-Jones
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
| | - Rikeish R. Muralitharan
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
- Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia (R.R.M.)
| | - Jane Muir
- Translational Nutrition Science in the Department of Gastroenterology, Central Clinical School (P.A.G., J.M., D.R-J.), Monash University, Melbourne, Australia
| | - Andrew Holmes
- Charles Perkin Centre and School of Life and Environmental Sciences, University of Sydney, Australia (A.H.)
| | - Charles R. Mackay
- Infection and Immunity Program, Monash Biomedicine Discovery Institute (C.R.M.), Monash University, Melbourne, Australia
- Department of Biochemistry and Molecular Biology (C.R.M.), Monash University, Melbourne, Australia
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