1
|
Wang Z, Lloyd D, Zhao S, Motsinger-Reif A. Taxanorm: a novel taxa-specific normalization approach for microbiome data. BMC Bioinformatics 2024; 25:304. [PMID: 39285319 PMCID: PMC11406911 DOI: 10.1186/s12859-024-05918-z] [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: 04/25/2024] [Accepted: 08/28/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND In high-throughput sequencing studies, sequencing depth, which quantifies the total number of reads, varies across samples. Unequal sequencing depth can obscure true biological signals of interest and prevent direct comparisons between samples. To remove variability due to differential sequencing depth, taxa counts are usually normalized before downstream analysis. However, most existing normalization methods scale counts using size factors that are sample specific but not taxa specific, which can result in over- or under-correction for some taxa. RESULTS We developed TaxaNorm, a novel normalization method based on a zero-inflated negative binomial model. This method assumes the effects of sequencing depth on mean and dispersion vary across taxa. Incorporating the zero-inflation part can better capture the nature of microbiome data. We also propose two corresponding diagnosis tests on the varying sequencing depth effect for validation. We find that TaxaNorm achieves comparable performance to existing methods in most simulation scenarios in downstream analysis and reaches a higher power for some cases. Specifically, it balances power and false discovery control well. When applying the method in a real dataset, TaxaNorm has improved performance when correcting technical bias. CONCLUSION TaxaNorm both sample- and taxon- specific bias by introducing an appropriate regression framework in the microbiome data, which aids in data interpretation and visualization. The 'TaxaNorm' R package is freely available through the CRAN repository https://CRAN.R-project.org/package=TaxaNorm and the source code can be downloaded at https://github.com/wangziyue57/TaxaNorm .
Collapse
Affiliation(s)
- Ziyue Wang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Dillon Lloyd
- Department of Biological Sciences and Statistics, North Carolina State University, Raleigh, NC, 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA.
| |
Collapse
|
2
|
Dalby MJ, Kiu R, Serghiou IR, Miyazaki A, Acford-Palmer H, Tung R, Caim S, Phillips S, Kujawska M, Matsui M, Iwamoto A, Taking B, Cox SE, Hall LJ. Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes. NPJ Biofilms Microbiomes 2024; 10:85. [PMID: 39277573 PMCID: PMC11401897 DOI: 10.1038/s41522-024-00562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 08/28/2024] [Indexed: 09/17/2024] Open
Abstract
The gut microbiota of infants in low- to middle-income countries is underrepresented in microbiome research. This study explored the faecal microbiota composition and faecal cytokine profiles in a cohort of infants in a rural province of Cambodia and investigated the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants were analysed for microbiota composition using 16S rRNA amplicon sequencing and concentrations of faecal cytokines. Faecal bacterial isolates were subjected to whole genome sequencing and genomic analysis. We compared the effects of two sample collection methods due to the challenges of faecal sample collection in a rural location. Storage of faecal samples in a DNA preservation solution preserved Bacteroides abundance. Microbiota analysis of preserved samples showed that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, with higher abundance in breast-fed infants. Most infants had detectable pathogenic taxa, with Shigella and Klebsiella more abundant in infants with recent diarrhoeal illness. Neither antibiotics nor infant growth were associated with gut microbiota composition. Genomic analysis of isolates showed gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and B. breve isolates. Antibiotic-resistant genes were present in both potentially pathogenic species and in Bifidobacterium. Faecal concentrations of Interlukin-1alpha and vascular endothelial growth factor were higher in breast-fed infants. This study provides insights into an underrepresented population of rural Cambodian infants, showing pathogen exposure and breastfeeding impact gut microbiota composition and faecal immune profiles.
Collapse
Affiliation(s)
- Matthew J Dalby
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Raymond Kiu
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Iliana R Serghiou
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Asuka Miyazaki
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Japan
| | - Holly Acford-Palmer
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Rathavy Tung
- National Maternal and Child Health Centre, Ministry of Health, Phnom Penh, Cambodia
| | - Shabhonam Caim
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Sarah Phillips
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Magdalena Kujawska
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, 80333, Germany
| | - Mitsuaki Matsui
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Japan
| | - Azusa Iwamoto
- Bureau of International Health Cooperation, National Centre for Global Health and Medicine, Tokyo, Japan
| | - Bunsreng Taking
- Kampong Cham Provincial Health Department, Ministry of Health, Kampong Cham, Cambodia
| | - Sharon E Cox
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Japan
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Lindsay J Hall
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK.
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
- Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, 80333, Germany.
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| |
Collapse
|
3
|
Tesfaw G, Siraj DS, Abdissa A, Jakobsen RR, Johansen ØH, Zangenberg M, Hanevik K, Mekonnen Z, Langeland N, Bjørang O, Safdar N, Mapes AC, Kates A, Krych L, Castro-Mejía JL, Nielsen DS. Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia. Nat Commun 2024; 15:7532. [PMID: 39223134 PMCID: PMC11369280 DOI: 10.1038/s41467-024-51464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Diarrhea claims >500,000 lives annually among children under five years of age in low- and middle-income countries. Mortality due to acute diarrhea (<7 days' duration) is decreasing, but prolonged (7-13 days) and persistent (≥14 days of duration) diarrhea remains a massive challenge. Here, we use a case-control study to decipher if fecal gut microbiota compositional differences between Ethiopian children with acute (n=554) or prolonged/persistent (n=95) diarrhea and frequency-matched non-diarrheal controls (n=663) are linked to diarrheal etiology. We show that diarrhea cases are associated with lower bacterial diversity and enriched in Escherichia spp., Campylobacter spp., and Streptococcus spp. Further, diarrhea cases are depleted in gut commensals such as Prevotella copri, Faecalibacterium prausnitzii, and Dialister succinatiphilus, with depletion being most pronounced in prolonged/persistent cases, suggesting that prolonged duration of diarrhea is accompanied by depletion of gut commensals and that re-establishing these via e.g., microbiota-directed food supplements offer a potential treatment strategy.
Collapse
Affiliation(s)
- Getnet Tesfaw
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia.
| | - Dawd S Siraj
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Alemseged Abdissa
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Øystein H Johansen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
- Microbiology Laboratory, Southern Health and Social Care Trust, Portadown, Northern Ireland
| | - Mike Zangenberg
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National Center for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Zeleke Mekonnen
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National Center for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ola Bjørang
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Nasia Safdar
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Abigail C Mapes
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Ashley Kates
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
4
|
Wang J, Ye H, Zhang C, Zhang A. Association of diarrhea or constipation with urinary incontinence in adults: A cross-sectional analysis of the National Health and Nutrition Examination Survey. Neurourol Urodyn 2024; 43:1674-1685. [PMID: 38693849 DOI: 10.1002/nau.25480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 05/03/2024]
Abstract
AIMS This study aimed to investigate the association between diarrhea or constipation and urinary incontinence (UI) in adults. METHODS Data from the National Health and Nutrition Examination Survey for 2009-2010 was used to include 4686 adults aged 20 and over in the analysis. Stress urinary incontinence (SUI) and urgency urinary incontinence (UUI) were used as outcome variables, with diarrhea and constipation as exposure factors. We first compared the baseline characteristics of those with and without SUI, as well as those with and without UUI. The impact of diarrhea or constipation on SUI and UUI was assessed using multivariate logistic regression models. To ensure the stability of the results, subgroup and stratified analyses were conducted. RESULTS The prevalence rates of UUI and SUI were 22.49% and 23.39%, respectively. Adjusted multivariate logistic regression analysis revealed that the risk of UUI was increased by either diarrhea (OR 1.66, 95% CI 1.36-2.04) or constipation (OR 1.42, 95% CI 1.11-1.83). The risk of SUI was also elevated by either diarrhea (OR 1.36, 95% CI 1.11-1.67) or constipation (OR 1.32, 95% CI 1.06-1.63). Subgroup analysis revealed no significant differences in the interaction tests between constipation or diarrhea and UI. CONCLUSIONS This study found that both constipation and diarrhea increase the risk of UUI and SUI.
Collapse
Affiliation(s)
- Junwei Wang
- Department of Urology, Wenling Hospital Affiliated to Wenzhou Medical University (The First People's Hospital of Wenling), Taizhou, Zhejiang, China
| | - Haibo Ye
- Department of Urology, Wenling Hospital Affiliated to Wenzhou Medical University (The First People's Hospital of Wenling), Taizhou, Zhejiang, China
| | - Cunming Zhang
- Department of Urology, Wenling Hospital Affiliated to Wenzhou Medical University (The First People's Hospital of Wenling), Taizhou, Zhejiang, China
| | - Aiwei Zhang
- Department of Ultrasound, Wenling Hospital Affiliated to Wenzhou Medical University (The First People's Hospital of Wenling), Taizhou, Zhejiang, China
| |
Collapse
|
5
|
Guitor AK, Katyukhina A, Mokomane M, Lechiile K, Goldfarb DM, Wright GD, McArthur AG, Pernica JM. Minimal Impact on the Resistome of Children in Botswana After Azithromycin Treatment for Acute Severe Diarrheal Disease. J Infect Dis 2024; 230:239-249. [PMID: 39052715 PMCID: PMC11272098 DOI: 10.1093/infdis/jiae049] [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: 08/28/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Macrolide antibiotics, including azithromycin, can reduce under 5 years of age mortality rates and treat various infections in children in sub-Saharan Africa. These exposures, however, can select for antibiotic-resistant bacteria in the gut microbiota. METHODS Our previous randomized controlled trial (RCT) of a rapid-test-and-treat strategy for severe acute diarrheal disease in children in Botswana included an intervention (3-day azithromycin dose) group and a control group that received supportive treatment. In this prospective matched cohort study using stools collected at baseline and 60 days after treatment from RCT participants, the collection of antibiotic resistance genes or resistome was compared between groups. RESULTS Certain macrolide resistance genes increased in prevalence by 13%-55% at 60 days, without differences in gene presence between the intervention and control groups. These genes were linked to tetracycline resistance genes and mobile genetic elements. CONCLUSIONS Azithromycin treatment for bacterial diarrhea for young children in Botswana resulted in similar effects on the gut resistome as the supportive treatment and did not provide additional selective pressure for macrolide resistance gene maintenance. The gut microbiota of these children contains diverse macrolide resistance genes that may be transferred within the gut upon repeated exposures to azithromycin or coselected by other antibiotics. CLINICAL TRIALS REGISTRATION NCT02803827.
Collapse
Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Anna Katyukhina
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Margaret Mokomane
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Botswana National Health Laboratory, Gaborone, Botswana
| | - Kwana Lechiile
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - David M Goldfarb
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Department of Pathology and Laboratory Medicine, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey M Pernica
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
6
|
Aragona SE, Spada C, DE Luca L, Aragona E, Ciprandi G. Probiotics for managing patients after bowel preparation for colonoscopy: an interventional, double-arm, open, randomized, multi-center, and national study (COLONSTUDY). Minerva Gastroenterol (Torino) 2024; 70:187-196. [PMID: 38818860 DOI: 10.23736/s2724-5985.24.03630-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
BACKGROUND Bowel preparation (BP) for colonoscopy induces significant changes in gut microbiota, causing dysbiosis that, in turn, elicits intestinal symptoms. Consequently, probiotics may counterbalance the disturbed microbiota after BP. So, probiotics may restore microbiota homeostasis. METHODS The current study evaluated the efficacy and safety of Abincol®, an oral nutraceutical containing a probiotic mixture with Lactobacillus plantarum LP01 (1 billion living cells), Lactobacillus lactis subspecies cremoris LLC02 (800 millions living cells), and Lactobacillus delbrueckii LDD01 (200 millions living cells), Patients were randomized in two groups (2:1). Group A took one stick/daily for four weeks after colonoscopy. Group B was considered as control. Patients were evaluated at baseline (T0) and after one (T1), two (T2), and four (T3) weeks. The severity of symptoms was measured by patients using a Visual Analog Scale. RESULTS Abincol® significantly diminished the presence and the severity of intestinal symptoms at T2 and even more at T3. All patients well tolerated the probiotic mixture. CONCLUSIONS The present study suggests that Abincol® may be considered an effective and safe therapeutic option in managing patients undergoing BP. The course should last one month.
Collapse
Affiliation(s)
- Salvatore E Aragona
- Unit of General Surgery, ASST Melegnano Martesana Presidio Melzo, Milan, Italy
| | - Cristiano Spada
- Unit of Digestive Endoscopy, IRCCS A. Gemelli University Polyclinic Foundation, Rome, Italy
| | - Luca DE Luca
- Unit of Gastroenterology and Digestive Endoscopy, ASST Santi Paolo e Carlo, Milan, Italy
| | - Elena Aragona
- Unit of General Surgery, ASST Melegnano Martesana Presidio Melzo, Milan, Italy
| | | |
Collapse
|
7
|
Jasuja JK, Bub F, Veit J, Fofana HKM, Sacko M, Saye R, Chatigre JK, N'Goran EK, Yao JA, Khanal B, Koirala K, Bhattarai NR, Rijal S, von Müller L, Bottieau E, Boelaert M, Chappuis F, Polman K, Utzinger J, Becker SL. Multiplex PCR for bacterial, viral and protozoal pathogens in persistent diarrhoea or persistent abdominal pain in Côte d'Ivoire, Mali and Nepal. Sci Rep 2024; 14:10926. [PMID: 38740833 DOI: 10.1038/s41598-024-60491-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
In contrast to acute diarrhoea, the aetiology of persistent digestive disorders (≥ 14 days) is poorly understood in low-resource settings and conventional diagnostic approaches lack accuracy. In this multi-country study, we compared multiplex real-time PCR for enteric bacterial, parasitic and viral pathogens in stool samples from symptomatic patients and matched asymptomatic controls in Côte d'Ivoire, Mali and Nepal. Among 1826 stool samples, the prevalence of most pathogens was highest in Mali, being up to threefold higher than in Côte d'Ivoire and up to tenfold higher than in Nepal. In all settings, the most prevalent bacteria were EAEC (13.0-39.9%) and Campylobacter spp. (3.9-35.3%). Giardia intestinalis was the predominant intestinal protozoon (2.9-20.5%), and adenovirus 40/41 was the most frequently observed viral pathogen (6.3-25.1%). Significantly different prevalences between symptomatic and asymptomatic individuals were observed for Campylobacter, EIEC and ETEC in the two African sites, and for norovirus in Nepal. Multiple species pathogen infection was common in Côte d'Ivoire and Mali, but rarely found in Nepal. We observed that molecular testing detected multiple enteric pathogens and showed low discriminatory accuracy to distinguish between symptomatic and asymptomatic individuals. Yet, multiplex PCR allowed for direct comparison between different countries and revealed considerable setting-specificity.
Collapse
Affiliation(s)
- Jasmin K Jasuja
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421, Homburg/Saar, Germany
- Department for Infectious Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Florian Bub
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421, Homburg/Saar, Germany
| | - Jonas Veit
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421, Homburg/Saar, Germany
| | | | - Moussa Sacko
- Institut National de Recherche en Santé Publique, Bamako, Mali
| | - Rénion Saye
- Institut National de Recherche en Santé Publique, Bamako, Mali
| | | | - Eliézer K N'Goran
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Joel A Yao
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Basudha Khanal
- Department of Microbiology, B P Koirala Institute of Health Sciences, Dharan, Nepal
| | - Kanika Koirala
- Department of Internal Medicine, B P Koirala Institute of Health Sciences, Dharan, Nepal
| | - Narayan R Bhattarai
- Department of Microbiology, B P Koirala Institute of Health Sciences, Dharan, Nepal
| | - Suman Rijal
- Department of Internal Medicine, B P Koirala Institute of Health Sciences, Dharan, Nepal
| | - Lutz von Müller
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421, Homburg/Saar, Germany
- Institute for Laboratory Medicine, Microbiology and Hygiene, Christophorus Kliniken, Coesfeld, Germany
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marleen Boelaert
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - François Chappuis
- Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Katja Polman
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421, Homburg/Saar, Germany.
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
| |
Collapse
|
8
|
Gandasegui J, Vergara A, Fleitas P, Rubio E, Fernandez-Pittol M, Aylagas C, Alvarez M, Zancada N, Camprubí-Ferrer D, Vila J, Muñoz J, Petrone P, Casals-Pascual C. Gut microbiota composition in travellers is associated with faecal lipocalin-2, a mediator of gut inflammation. Front Cell Infect Microbiol 2024; 14:1387126. [PMID: 38736752 PMCID: PMC11082338 DOI: 10.3389/fcimb.2024.1387126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction We examined the gut microbiota of travellers returning from tropical areas with and without traveller's diarrhoea (TD) and its association with faecal lipocalin-2 (LCN2) levels. Methods Participants were recruited at the Hospital Clinic of Barcelona, Spain, and a single stool sample was collected from each individual to perform the diagnostic of the etiological agent causing gastrointestinal symptoms as well as to measure levels of faecal LCN2 as a biomarker of gut inflammation. We also characterised the composition of the gut microbiota by sequencing the region V3-V4 from the 16S rRNA gene, and assessed its relation with the clinical presentation of TD and LCN2 levels using a combination of conventional statistical tests and unsupervised machine learning approaches. Results Among 61 participants, 45 had TD, with 40% having identifiable etiological agents. Surprisingly, LCN2 levels were similar across groups, suggesting gut inflammation occurs without clinical TD symptoms. Differential abundance (DA) testing highlighted a microbial profile tied to high LCN2 levels, marked by increased Proteobacteria and Escherichia-Shigella, and decreased Firmicutes, notably Oscillospiraceae. UMAP analysis confirmed this profile's association, revealing distinct clusters based on LCN2 levels. The study underscores the discriminatory power of UMAP in capturing meaningful microbial patterns related to clinical variables. No relevant differences in the gut microbiota composition were found between travellers with or without TD. Discussion The findings suggest a correlation between gut microbiome and LCN2 levels during travel, emphasising the need for further research to discern the nature of this relationship.
Collapse
Affiliation(s)
| | - Andrea Vergara
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
| | - Pedro Fleitas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Elisa Rubio
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Mariana Fernandez-Pittol
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Cristian Aylagas
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Míriam Alvarez
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Noelia Zancada
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Daniel Camprubí-Ferrer
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Tropical Medicine and International Health Department, Hospital Clínic, Barcelona, Spain
| | - Jordi Vila
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
| | - José Muñoz
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
- Tropical Medicine and International Health Department, Hospital Clínic, Barcelona, Spain
| | - Paula Petrone
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Climent Casals-Pascual
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
| |
Collapse
|
9
|
Le SNH, Nguyen Ngoc Minh C, de Sessions PF, Jie S, Tran Thi Hong C, Thwaites GE, Baker S, Pham DT, Chung The H. The impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:12. [PMID: 38686335 PMCID: PMC11057199 DOI: 10.1038/s44259-024-00030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/15/2024] [Indexed: 05/02/2024]
Abstract
Infectious diarrhoeal diseases remain a substantial health burden in young children in low- and middle-income countries. The disease and its variable treatment options significantly alter the gut microbiome, which may affect clinical outcomes and overall gut health. Antibiotics are often prescribed, but their impact on the gut microbiome during recovery is unclear. Here, we used 16S rRNA sequencing to investigate changes in the gut microbiota in Vietnamese children with acute watery diarrhoea, and highlight the impact of antibiotic treatment on these changes. Our analyses identified that, regardless of treatment, recovery was characterised by reductions in Streptococcus and Rothia species and expansion of Bacteroides/Phocaeicola, Lachnospiraceae and Ruminococcacae taxa. Antibiotic treatment significantly delayed the temporal increases in alpha- and beta-diversity within patients, resulting in distinctive patterns of taxonomic change. These changes included a pronounced, transient overabundance of Enterococcus species and depletion of Bifidobacterium pseudocatenulatum. Our findings demonstrate that antibiotic treatment slows gut microbiota recovery in children following watery diarrhoea.
Collapse
Affiliation(s)
- Son-Nam H. Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | | | | | - Song Jie
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| |
Collapse
|
10
|
Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
Collapse
Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
11
|
Muralidharan HS, Fox NY, Pop M. The impact of transitive annotation on the training of taxonomic classifiers. Front Microbiol 2024; 14:1240957. [PMID: 38235435 PMCID: PMC10792039 DOI: 10.3389/fmicb.2023.1240957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/03/2023] [Indexed: 01/19/2024] Open
Abstract
Introduction A common task in the analysis of microbial communities involves assigning taxonomic labels to the sequences derived from organisms found in the communities. Frequently, such labels are assigned using machine learning algorithms that are trained to recognize individual taxonomic groups based on training data sets that comprise sequences with known taxonomic labels. Ideally, the training data should rely on labels that are experimentally verified-formal taxonomic labels require knowledge of physical and biochemical properties of organisms that cannot be directly inferred from sequence alone. However, the labels associated with sequences in biological databases are most commonly computational predictions which themselves may rely on computationally-generated data-a process commonly referred to as "transitive annotation." Methods In this manuscript we explore the implications of training a machine learning classifier (the Ribosomal Database Project's Bayesian classifier in our case) on data that itself has been computationally generated. We generate new training examples based on 16S rRNA data from a metagenomic experiment, and evaluate the extent to which the taxonomic labels predicted by the classifier change after re-training. Results We demonstrate that even a few computationally-generated training data points can significantly skew the output of the classifier to the point where entire regions of the taxonomic space can be disturbed. Discussion and conclusions We conclude with a discussion of key factors that affect the resilience of classifiers to transitively-annotated training data, and propose best practices to avoid the artifacts described in our paper.
Collapse
Affiliation(s)
- Harihara Subrahmaniam Muralidharan
- Department of Computer Science, University of Maryland, College Park, MD, United States
- Center for Bioinformatics and Computational Biology (CBCB), University of Maryland, College Park, MD, United States
| | - Noam Y. Fox
- Department of Computer Science, University of Maryland, College Park, MD, United States
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, United States
- Center for Bioinformatics and Computational Biology (CBCB), University of Maryland, College Park, MD, United States
| |
Collapse
|
12
|
Jesser KJ, Trueba G, Konstantinidis KT, Levy K. Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador. Gut Microbes 2023; 15:2281010. [PMID: 37992406 PMCID: PMC10730187 DOI: 10.1080/19490976.2023.2281010] [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] [Received: 05/31/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.
Collapse
Affiliation(s)
- Kelsey J Jesser
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
13
|
Dhivahar J, Parthasarathy A, Krishnan K, Kovi BS, Pandian GN. Bat-associated microbes: Opportunities and perils, an overview. Heliyon 2023; 9:e22351. [PMID: 38125540 PMCID: PMC10730444 DOI: 10.1016/j.heliyon.2023.e22351] [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: 07/14/2022] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.
Collapse
Affiliation(s)
- J. Dhivahar
- Research Department of Zoology, St. Johns College, Palayamkottai, 627002, India
- Department of Plant Biology and Biotechnology, Laboratory of Microbial Ecology, Loyola College, Chennai, 600034, India
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Anutthaman Parthasarathy
- Department of Chemistry and Biosciences, Richmond Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Kathiravan Krishnan
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Basavaraj S. Kovi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| |
Collapse
|
14
|
Hoek KL, McClanahan KG, Latour YL, Shealy N, Piazuelo MB, Vallance BA, Byndloss MX, Wilson KT, Olivares-Villagómez D. Turicibacterales protect mice from severe Citrobacter rodentium infection. Infect Immun 2023; 91:e0032223. [PMID: 37800916 PMCID: PMC10652940 DOI: 10.1128/iai.00322-23] [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: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
One of the major contributors to child mortality in the world is diarrheal diseases, with an estimated 800,000 deaths per year. Many pathogens are causative agents of these illnesses, including the enteropathogenic or enterohemorrhagic forms of Escherichia coli. These bacteria are characterized by their ability to cause attaching and effacing lesions in the gut mucosa. Although much has been learned about the pathogenicity of these organisms and the immune response against them, the role of the intestinal microbiota during these infections is not well characterized. Infection of mice with E. coli requires pre-treatment with antibiotics in most mouse models, which hinders the study of the microbiota in an undisturbed environment. Using Citrobacter rodentium as a murine model for attaching and effacing bacteria, we show that C57BL/6 mice deficient in granzyme B expression are highly susceptible to severe disease caused by C. rodentium infection. Although a previous publication from our group shows that granzyme B-deficient CD4+ T cells are partially responsible for this phenotype, in this report, we present data demonstrating that the microbiota, in particular members of the order Turicibacterales, have an important role in conferring resistance. Mice deficient in Turicibacter sanguinis have increased susceptibility to severe disease. However, when these mice are co-housed with resistant mice or colonized with T. sanguinis, susceptibility to severe infection is reduced. These results clearly suggest a critical role for this commensal in the protection against enteropathogens.
Collapse
Affiliation(s)
- Kristen L. Hoek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathleen G. McClanahan
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yvonne L. Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicolas Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bruce A. Vallance
- Department of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Microbiome Innovation Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T. Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veternas Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Danyvid Olivares-Villagómez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
15
|
De Silva PM, Bennett RJ, Kuhn L, Ngondo P, Debande L, Njamkepo E, Ho B, Weill FX, Marteyn BS, Jenkins C, Baker KS. Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins. EBioMedicine 2023; 97:104822. [PMID: 37806286 PMCID: PMC10579285 DOI: 10.1016/j.ebiom.2023.104822] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei. METHODS We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics. FINDINGS Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent. INTERPRETATION Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings. FUNDING Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.
Collapse
Affiliation(s)
- P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Rebecca J Bennett
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Patryk Ngondo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Lorine Debande
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Brian Ho
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Benoît S Marteyn
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, Colindale, London, UK
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom; Department of Genetics, University of Cambridge, Downing Place, Cambridge, UK.
| |
Collapse
|
16
|
Witt RG, Cass SH, Tran T, Damania A, Nelson EE, Sirmans E, Burton EM, Chelvanambi M, Johnson S, Tawbi HA, Gershenwald JE, Davies MA, Spencer C, Mishra A, Wong MC, Ajami NJ, Peterson CB, Daniel CR, Wargo JA, McQuade JL, Nelson KC. Gut Microbiome in Patients With Early-Stage and Late-Stage Melanoma. JAMA Dermatol 2023; 159:1076-1084. [PMID: 37647056 PMCID: PMC10469295 DOI: 10.1001/jamadermatol.2023.2955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/20/2023] [Indexed: 09/01/2023]
Abstract
Importance The gut microbiome modulates the immune system and responses to immunotherapy in patients with late-stage melanoma. It is unknown whether fecal microbiota profiles differ between healthy individuals and patients with melanoma or if microbiota profiles differ among patients with different stages of melanoma. Defining gut microbiota profiles in individuals without melanoma and those with early-stage and late-stage melanoma may reveal features associated with disease progression. Objective To characterize and compare gut microbiota profiles between healthy volunteers and patients with melanoma and between patients with early-stage and late-stage melanoma. Design, Setting, and Participants This single-site case-control study took place at an academic comprehensive cancer center. Fecal samples were collected from systemic treatment-naive patients with stage I to IV melanoma from June 1, 2015, to January 31, 2019, and from healthy volunteers from June 1, 2021, to January 31, 2022. Patients were followed up for disease recurrence until November 30, 2021. Main Outcomes and Measures Fecal microbiota was profiled by 16S ribosomal RNA sequencing. Clinical and pathologic characteristics, treatment, and disease recurrence were extracted from electronic medical records. Fecal microbiome diversity, taxonomic profiles and inferred functional profiles were compared between groups. Results A total of 228 participants were enrolled (126 men [55.3%]; median age, 59 [range, 21-90] years), including 49 volunteers without melanoma, 38 patients with early-stage melanoma (29 with stage I or melanoma in situ and 9 with stage II), and 141 with late-stage melanoma (66 with stage III and 75 with stage IV). Community differences were observed between patients with melanoma and volunteers. Patients with melanoma had a higher relative abundance of Fusobacterium compared with controls on univariate analysis (0.19% vs 0.003%; P < .001), but this association was attenuated when adjusted for covariates (log2 fold change of 5.18 vs controls; P = .09). Microbiomes were distinct between patients with early-stage and late-stage melanoma. Early-stage melanoma had a higher alpha diversity (Inverse Simpson Index 14.6 [IQR, 9.8-23.0] vs 10.8 [IQR, 7.2-16.8]; P = .003), and a higher abundance of the genus Roseburia on univariate analysis (2.4% vs 1.2%; P < .001) though statistical significance was lost with covariate adjustment (log2 fold change of 0.86 vs controls; P = .13). Multiple functional pathways were differentially enriched between groups. No associations were observed between the microbial taxa and disease recurrence in patients with stage III melanoma treated with adjuvant immunotherapy. Conclusions and Relevance The findings of this case-control study suggest that fecal microbiota profiles were significantly different among patients with melanoma and controls and between patients with early-stage and late-stage melanoma. Prospective investigations of the gut microbiome and changes that occur with disease progression may identify future microbial targets for intervention.
Collapse
Affiliation(s)
- Russell G. Witt
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Samuel H. Cass
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Tiffaney Tran
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston
| | - Ashish Damania
- Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Emelie E. Nelson
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Elizabeth Sirmans
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Elizabeth M. Burton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Manoj Chelvanambi
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Sarah Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Jeffrey E. Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Christine Spencer
- Department of Informatics, Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Aditya Mishra
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Matthew C. Wong
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Nadim J. Ajami
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Christine B. Peterson
- Department of Biostatistics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston
| | - Carrie R. Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer L. McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Kelly C. Nelson
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston
| |
Collapse
|
17
|
Du Z, Li J, Li W, Fu H, Ding J, Ren G, Zhou L, Pi X, Ye X. Effects of prebiotics on the gut microbiota in vitro associated with functional diarrhea in children. Front Microbiol 2023; 14:1233840. [PMID: 37720150 PMCID: PMC10502507 DOI: 10.3389/fmicb.2023.1233840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 09/19/2023] Open
Abstract
Purpose Diarrhea is among the top five causes of morbidity and mortality in children. Dysbiosis of the gut microbiota is considered the most important risk factor for diarrhea. Prebiotics have shown efficacy in treating diarrhea by regulating the balance of the gut microbiota in vivo. Methods In this study, we used an in vitro fermentation system to prevent the interference of host-gut microbe interactions during in vivo examination and investigated the effect of fructo-oligosaccharides (FOS) on gut microbiota composition and metabolism in 39 pediatric patients with functional diarrhea. Results 16S rRNA sequencing revealed that FOS significantly improved α- and β-diversity in volunteers with pediatric diarrhea (p < 0.05). This improvement manifested as a significant increase (LDA > 2, p < 0.05) in probiotic bacteria (e.g., Bifidobacterium) and a significant inhibition (LDA > 2, p < 0.05) of harmful bacteria (e.g., Escherichia-Shigella). Notably, the analysis of bacterial metabolites after FOS treatment showed that the decrease in isobutyric acid, isovaleric acid, NH3, and H2S levels was positively correlated with the relative abundance of Lachnoclostridium. This decrease also showed the greatest negative correlation with the abundance of Streptococcus. Random forest analysis and ROC curve validation demonstrated that gut microbiota composition and metabolites were distinct between the FOS treatment and control groups (area under the curve [AUC] > 0.8). Functional prediction using PICRUSt 2 revealed that the FOS-induced alteration of gut microbiota was most likely mediated by effects on starch and sucrose metabolism. Conclusion This study is the first to evince that FOS can modulate gut microbial disorders in children with functional diarrhea. Our findings provide a framework for the application of FOS to alleviate functional diarrhea in children and reduce the use of antibiotics for managing functional diarrhea-induced disturbances in the gut microbiota.
Collapse
Affiliation(s)
- Zhi Du
- Department of Pharmacy, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Research Center for Clinical Pharmacy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiabin Li
- Department of Pharmacy, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Research Center for Clinical Pharmacy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Li
- Department of Clinical Laboratory, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Hao Fu
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jieying Ding
- Department of Pharmacy, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Research Center for Clinical Pharmacy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Guofei Ren
- Department of Pharmacy, Zhejiang Xiaoshan Hospital, Hangzhou, Zhejiang, China
| | - Linying Zhou
- People's Hospital of Longquan City, Longquan, China
| | - Xionge Pi
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaoli Ye
- Department of Medical Administration, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| |
Collapse
|
18
|
Iancu MA, Profir M, Roşu OA, Ionescu RF, Cretoiu SM, Gaspar BS. Revisiting the Intestinal Microbiome and Its Role in Diarrhea and Constipation. Microorganisms 2023; 11:2177. [PMID: 37764021 PMCID: PMC10538221 DOI: 10.3390/microorganisms11092177] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
The gut microbiota represents a community of microorganisms (bacteria, fungi, archaea, viruses, and protozoa) that colonize the gut and are responsible for gut mucosal structural integrity and immune and metabolic homeostasis. The relationship between the gut microbiome and human health has been intensively researched in the past years. It is now widely recognized that gut microbial composition is highly responsible for the general health of the host. Among the diseases that have been linked to an altered gut microbial population are diarrheal illnesses and functional constipation. The capacity of probiotics to modulate the gut microbiome population, strengthen the intestinal barrier, and modulate the immune system together with their antioxidant properties have encouraged the research of probiotic therapy in many gastrointestinal afflictions. Dietary and lifestyle changes and the use of probiotics seem to play an important role in easing constipation and effectively alleviating diarrhea by suppressing the germs involved. This review aims to describe how probiotic bacteria and the use of specific strains could interfere and bring benefits as an associated treatment for diarrhea and constipation.
Collapse
Affiliation(s)
- Mihaela Adela Iancu
- Department of Family Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Monica Profir
- Department of Oncology, Elias University Emergency Hospital, 011461 Bucharest, Romania; (M.P.); (O.A.R.)
| | - Oana Alexandra Roşu
- Department of Oncology, Elias University Emergency Hospital, 011461 Bucharest, Romania; (M.P.); (O.A.R.)
| | - Ruxandra Florentina Ionescu
- Department of Morphological Sciences, Cell and Molecular Biology and Histology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
- Department of Cardiology I, “Dr. Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania
| | - Sanda Maria Cretoiu
- Department of Morphological Sciences, Cell and Molecular Biology and Histology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Bogdan Severus Gaspar
- Surgery Clinic, Emergency Clinical Hospital, 014461 Bucharest, Romania;
- Department of Surgery, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| |
Collapse
|
19
|
Mangiola S, Roth-Schulze AJ, Trussart M, Zozaya-Valdés E, Ma M, Gao Z, Rubin AF, Speed TP, Shim H, Papenfuss AT. sccomp: Robust differential composition and variability analysis for single-cell data. Proc Natl Acad Sci U S A 2023; 120:e2203828120. [PMID: 37549298 PMCID: PMC10438834 DOI: 10.1073/pnas.2203828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/18/2023] [Indexed: 08/09/2023] Open
Abstract
Cellular omics such as single-cell genomics, proteomics, and microbiomics allow the characterization of tissue and microbial community composition, which can be compared between conditions to identify biological drivers. This strategy has been critical to revealing markers of disease progression, such as cancer and pathogen infection. A dedicated statistical method for differential variability analysis is lacking for cellular omics data, and existing methods for differential composition analysis do not model some compositional data properties, suggesting there is room to improve model performance. Here, we introduce sccomp, a method for differential composition and variability analyses that jointly models data count distribution, compositionality, group-specific variability, and proportion mean-variability association, being aware of outliers. sccomp provides a comprehensive analysis framework that offers realistic data simulation and cross-study knowledge transfer. Here, we demonstrate that mean-variability association is ubiquitous across technologies, highlighting the inadequacy of the very popular Dirichlet-multinomial distribution. We show that sccomp accurately fits experimental data, significantly improving performance over state-of-the-art algorithms. Using sccomp, we identified differential constraints and composition in the microenvironment of primary breast cancer.
Collapse
Affiliation(s)
- Stefano Mangiola
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC3052, Australia
| | - Alexandra J. Roth-Schulze
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC3052, Australia
| | - Marie Trussart
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
| | - Enrique Zozaya-Valdés
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC3052, Australia
| | - Mengyao Ma
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
| | - Zijie Gao
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC3052, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC3052, Australia
| | - Alan F. Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC3052, Australia
| | - Terence P. Speed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
| | - Heejung Shim
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC3052, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC3052, Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC3052, Australia
| |
Collapse
|
20
|
Fan Q, Du E, Chen F, Tao W, Zhao N, Huang S, Guo W, Huang J, Wei J. Maternal Magnolol Supplementation during Pregnancy and Lactation Promotes Antioxidant Capacity, Improves Gut Health, and Alters Gut Microbiota and Metabolites of Weanling Piglets. Metabolites 2023; 13:797. [PMID: 37512505 PMCID: PMC10383630 DOI: 10.3390/metabo13070797] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Maternal nutrition exerts a profound effect on the postnatal performance of offspring, especially during the weaning period. The multifunctional bioactive component magnolol (MAG) has shown promise as a dietary supplement. This study aimed to explore the effects of maternal MAG supplementation on the antioxidant capacity, gut health, gut microbiome, and metabolome composition of weanling piglets. Fifty pregnant sows were randomly divided into two equally sized groups, the control group and the group supplemented with 100 g/t MAG during the gestation and lactation periods, and 7 days postweaning, the pups were euthanized. The microbiome and metabolome features of weanling piglet colons were compared. Our results revealed that maternal MAG supplementation modified the serum redox status of weanling piglets by decreasing malondialdehyde concentration and increasing superoxide dismutase activity and total antioxidant capacity. Moreover, the decreased indicators of diarrhea were accompanied by improved gut barrier function, in which serum diamine oxidase concentration was decreased, and expressions of zona occludens-1, claudin-1, and intestinal alkaline phosphatase were increased in the colon of weanling piglets from sows supplemented with MAG. Further analysis of the gut microbiota indicated that maternal MAG supplementation significantly increased the relative abundance of beneficial bacteria in the colon of weanling piglets, including Faecalibacterium prausnitzii and Oscillospira. Metabolome analysis identified 540 differential metabolites in the colon of piglets from MAG-fed dams, of which glycerophospholipid classes were highly correlated with progeny gut health and key beneficial bacteria. Our findings indicated that maternal MAG supplementation can improve the oxidative status and gut health of weanling piglets, possibly due to alterations in the gut microbiota and metabolites.
Collapse
Affiliation(s)
- Qiwen Fan
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Encun Du
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Fang Chen
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Wenjing Tao
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Na Zhao
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Shaowen Huang
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Wanzheng Guo
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Jing Huang
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Jintao Wei
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| |
Collapse
|
21
|
Yousefi B, Melograna F, Galazzo G, van Best N, Mommers M, Penders J, Schwikowski B, Van Steen K. Capturing the dynamics of microbial interactions through individual-specific networks. Front Microbiol 2023; 14:1170391. [PMID: 37256048 PMCID: PMC10225591 DOI: 10.3389/fmicb.2023.1170391] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023] Open
Abstract
Longitudinal analysis of multivariate individual-specific microbiome profiles over time or across conditions remains dauntin. Most statistical tools and methods that are available to study microbiomes are based on cross-sectional data. Over the past few years, several attempts have been made to model the dynamics of bacterial species over time or across conditions. However, the field needs novel views on handling microbial interactions in temporal analyses. This study proposes a novel data analysis framework, MNDA, that combines representation learning and individual-specific microbial co-occurrence networks to uncover taxon neighborhood dynamics. As a use case, we consider a cohort of newborns with microbiomes available at 6 and 9 months after birth, and extraneous data available on the mode of delivery and diet changes between the considered time points. Our results show that prediction models for these extraneous outcomes based on an MNDA measure of local neighborhood dynamics for each taxon outperform traditional prediction models solely based on individual-specific microbial abundances. Furthermore, our results show that unsupervised similarity analysis of newborns in the study, again using the notion of a taxon's dynamic neighborhood derived from time-matched individual-specific microbial networks, can reveal different subpopulations of individuals, compared to standard microbiome-based clustering, with potential relevance to clinical practice. This study highlights the complementarity of microbial interactions and abundances in downstream analyses and opens new avenues to personalized prediction or stratified medicine with temporal microbiome data.
Collapse
Affiliation(s)
- Behnam Yousefi
- Computational Systems Biomedicine Lab, Institut Pasteur, University Paris City, Paris, France
- École Doctorale Complexite du vivant, Sorbonne University, Paris, France
- BIO3—Laboratory for Systems Medicine, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Federico Melograna
- BIO3—Laboratory for Systems Medicine, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gianluca Galazzo
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Niels van Best
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, Netherlands
- Institute of Medical Microbiology, Rhine-Westphalia Technical University of Aachen, RWTH University, Aachen, Germany
| | - Monique Mommers
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Benno Schwikowski
- Computational Systems Biomedicine Lab, Institut Pasteur, University Paris City, Paris, France
| | - Kristel Van Steen
- BIO3—Laboratory for Systems Medicine, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- BIO3—Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Lièvzge, Liège, Belgium
| |
Collapse
|
22
|
Zhan M, Liang X, Chen J, Yang X, Han Y, Zhao C, Xiao J, Cao Y, Xiao H, Song M. Dietary 5-demethylnobiletin prevents antibiotic-associated dysbiosis of gut microbiota and damage to the colonic barrier. Food Funct 2023; 14:4414-4429. [PMID: 37097253 DOI: 10.1039/d3fo00516j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
5-Demethylnobiletin (5DN) is an important ingredient of citrus extract that is rich in polymethoxyflavones (PMFs). In this study, we systemically investigated the preventive effects of 5DN on antibiotic-associated intestinal disturbances. Experimental mice were gavaged 0.2 mL per day of the antibiotic cocktail (12.5 g L-1 cefuroxime and 10 g L-1 levofloxacin) for 10 days, accompanied by dietary 0.05% 5DN for 10 and 20 days. The results showed that the combination of cefuroxime and levofloxacin caused swelling of the cecum and injury to the colon tissue. Meanwhile, the balance of intestinal oxidative stress and the barrier function of mice was also damaged by the antibiotics through upregulation of the relative mRNA levels of superoxide dismutase 3 (SOD3), quinine oxidoreductase 1 (NQO1) and glutathione peroxidase 1 (GPX1), and downregulation of the relative protein levels of tight junction proteins (TJs). Moreover, antibiotic exposure led to disorder of the gut microbiota, particularly increased harmful bacteria (Proteobacteria) and decreased beneficial bacteria (Bacteroideta). However, dietary 5DN could reduce antibiotic-associated intestinal damage, evidenced by the results that 5DN alleviated gut oxidative damage and attenuated intestinal barrier injury via increasing the expression of TJs including occludin and zonula occluden1 (ZO1). Additionally, dietary 5DN modulated the composition of the gut microbiota in antibiotic-treated mice by increasing the relative levels of beneficial bacteria, such as Dubosiella and Lactobacillus. Moreover, PMFs increased the contents of isobutyric acid and butyric acid, which were almost eliminated by antibiotic exposure. In conclusion, 5DN could alleviate antibiotic-related imbalance of intestinal oxidative stress, barrier function damage, intestinal flora disorders and the reduction of short-chain fatty acids (SCFAs), which lays a foundation for exploring safer and more effective ways to prevent or mitigate antibiotic-associated intestinal damage.
Collapse
Affiliation(s)
- Minmin Zhan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| | - Xinyan Liang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| | - Jiaqi Chen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| | - Xiaoshuang Yang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| | - Yanhui Han
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Chenxi Zhao
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Jie Xiao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Mingyue Song
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Sciences, South China Agricultural University, Guangzhou, China.
| |
Collapse
|
23
|
Hoek KL, McClanahan KG, Latour YL, Shealy N, Piazuelo MB, Vallance BA, Byndloss MX, Wilson KT, Olivares-Villagómez D. Turicibacterales protect mice from severe Citrobacter rodentium infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538270. [PMID: 37163036 PMCID: PMC10168287 DOI: 10.1101/2023.04.25.538270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
One of the major contributors to child mortality in the world is diarrheal diseases, with an estimated 800,000 deaths per year. Many pathogens are causative agents of these illnesses, including the enteropathogenic (EPEC) or enterohemorrhagic (EHEC) forms of Escherichia coli. These bacteria are characterized by their ability to cause attaching and effacing lesions in the gut mucosa. Although much has been learned about the pathogenicity of these organisms and the immune response against them, the role of the intestinal microbiota during these infections is not well characterized. Infection of mice with E. coli requires pre-treatment with antibiotics in most mouse models, which hinders the study of the microbiota in an undisturbed environment. Using Citrobacter rodentium as a murine model for attaching and effacing bacteria, we show that C57BL/6 mice deficient in granzyme B expression are highly susceptible to severe disease caused by C. rodentium infection. Although a previous publication from our group shows that granzyme B-deficient CD4+ T cells are partially responsible for this phenotype, in this report we present data demonstrating that the microbiota, in particular members of the order Turicibacterales, have an important role in conferring resistance. Mice deficient in Turicibacter sanguinis have increased susceptibility to severe disease. However, when these mice are co-housed with resistant mice, or colonized with T. sanguinis, susceptibility to severe infection is reduced. These results clearly suggest a critical role for this commensal in the protection against entero-pathogens.
Collapse
Affiliation(s)
- Kristen L. Hoek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathleen G. McClanahan
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yvonne L. Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicolas Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bruce A. Vallance
- Department of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Microbiome Innovation Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Veternas Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Danyvid Olivares-Villagómez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
24
|
Sajnaga E, Socała K, Kalwasińska A, Wlaź P, Waśko A, Jach ME, Tomczyk M, Wiater A. Response of murine gut microbiota to a prebiotic based on oligosaccharides derived via hydrolysis of fungal α-(1→3)-d-glucan: Preclinical trial study on mice. Food Chem 2023; 417:135928. [PMID: 36933426 DOI: 10.1016/j.foodchem.2023.135928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 02/04/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
We investigated the modulating effect of α-(1→3)-glucooligosaccharides (GOS), i.e. a product of fungal α-(1→3)-d-glucan hydrolysis, on the gut microbiota composition. Mice were fed with a GOS-supplemented diet and two control diets for 21 days, and fecal samples were collected at 0, 1, and 3-week time points. The bacterial community composition was determined by 16S rRNA gene Illumina sequencing. The gut microbiota of the GOS-supplemented mice showed profound time-dependent changes in the taxonomic composition; however, we did not observe significant changes in α-diversity indices. The biggest number of genus abundance shifts after 1 week of the treatment was noticed between the group of the GOS-supplemented mice and the controls; however, the differences were still relevant after the 3-week treatment. The GOS-supplemented mice displayed higher abundance of Prevotella spp., with a concomitant decrease in the abundance of Escherichia-Shigella. Hence, GOS seems to be a promising candidate for a new prebiotic.
Collapse
Affiliation(s)
- Ewa Sajnaga
- Department of Biomedicine and Environmental Research, John Paul II Catholic University of Lublin, ul. Konstantynów 1J, 20-708 Lublin, Poland
| | - Katarzyna Socała
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, ul. Lwowska 1, 87-100 Toruń, Poland
| | - Piotr Wlaź
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland
| | - Adam Waśko
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, ul. Skromna 8, 20-704 Lublin, Poland
| | - Monika Elżbieta Jach
- Department of Molecular Biology, John Paul II Catholic University of Lublin, ul. Konstantynów 1H, 20-708 Lublin, Poland
| | - Michał Tomczyk
- Department of Pharmacognosy, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2a, 15-230 Białystok, Poland
| | - Adrian Wiater
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland.
| |
Collapse
|
25
|
Balaji V, Dinh DM, Kane AV, Soofi S, Ahmed I, Rizvi A, Chatterjee M, Babji S, Duara J, Moy J, Naumova EN, Wanke CA, Ward HD, Bhutta ZA. Longitudinal Analysis of the Intestinal Microbiota among a Cohort of Children in Rural and Urban Areas of Pakistan. Nutrients 2023; 15:1213. [PMID: 36904212 PMCID: PMC10005232 DOI: 10.3390/nu15051213] [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: 12/06/2022] [Revised: 02/09/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
The profile of the intestinal microbiota is known to be altered in malnourished young children in low- and middle-income countries. However, there are limited studies longitudinally evaluating the intestinal microbiota in malnourished young children in resource-limited settings over the first two years of life. In this longitudinal pilot study, we determined the effect of age, residential location, and intervention on the composition, relative abundance, and diversity of the intestinal microbiota in a representative sample of children under 24 months of age with no diarrhea in the preceding 72 h in the urban and rural areas of Sindh, Pakistan nested within a cluster-randomized trial evaluating the effect of zinc and micronutrients on growth and morbidity (ClinicalTrials.gov Identifier: NCT00705445). The major findings were age-related with significant changes in alpha and beta diversity with increasing age. There was a significant increase in the relative abundance of the Firmicutes and Bacteroidetes phyla and a significant decrease in that of the Actinobacteria and Proteobacteria phyla (p < 0.0001). There were significant increases in the relative abundances of the major genera Bifidobacterium, Escherichia/Shigella and Streptococcus (p < 0.0001), and no significant change in the relative abundance of Lactobacillus. Using the LEfSE algorithm, differentially abundant taxa were identified between children in the first and second years of age, between those residing in rural and urban areas, and those who received different interventions at different ages from 3 to 24 months. The numbers of malnourished (underweight, wasted, stunted) or well-nourished children at each age, in each intervention arm, and at urban or rural sites were too small to determine if there were significant differences in alpha or beta diversity or differentially abundant taxa among them. Further longitudinal studies with larger numbers of well-nourished and malnourished children are required to fully characterize the intestinal microbiota of children in this region.
Collapse
Affiliation(s)
- Veeraraghavan Balaji
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Microbiology, Christian Medical College, Vellore 632004, India
| | - Duy M. Dinh
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Anne V. Kane
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Sajid Soofi
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | - Imran Ahmed
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | - Arjumand Rizvi
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | - Meera Chatterjee
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Sudhir Babji
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Microbiology, Christian Medical College, Vellore 632004, India
| | - Joanne Duara
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Joy Moy
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Elena N. Naumova
- Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Christine A. Wanke
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Honorine D. Ward
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Zulfiqar A. Bhutta
- Division of Nutrition Data Sciences, Center of Excellence in Women and Child Health, The Aga Khan University, Karachi 74800, Pakistan
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 3E2, Canada
| |
Collapse
|
26
|
Banaszak M, Górna I, Woźniak D, Przysławski J, Drzymała-Czyż S. Association between Gut Dysbiosis and the Occurrence of SIBO, LIBO, SIFO and IMO. Microorganisms 2023; 11:573. [PMID: 36985147 PMCID: PMC10052891 DOI: 10.3390/microorganisms11030573] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Gut microbiota is the aggregate of all microorganisms in the human digestive system. There are 1014 CFU/mL of such microorganisms in the human body, including bacteria, viruses, fungi, archaea and protozoa. The Firmicutes and Bacteroidetes bacteria phyla comprise 90% of the human gut microbiota. The microbiota support the healthy functioning of the human body by helping with digestion (mainly via short-chain fatty acids and amino acids) and producing short-chain fatty acids. In addition, it exhibits many physiological functions, such as forming the intestinal epithelium, intestinal integrity maintenance, the production of vitamins, and protection against pathogens. An altered composition or the number of microorganisms, known as dysbiosis, disrupts the body's homeostasis and can lead to the development of inflammatory bowel disease, irritable bowel syndrome, and metabolic diseases such as diabetes, obesity and allergies. Several types of disruptions to the gut microbiota have been identified: SIBO (Small Intestinal Bacterial Overgrowth), LIBO (Large Intestinal Bacterial Overgrowth), SIFO (Small Intestinal Fungal Overgrowth), and IMO (Intestinal Methanogen Overgrowth). General gastrointestinal problems such as abdominal pain, bloating, gas, diarrhoea and constipation are the main symptoms of dysbiosis. They lead to malabsorption, nutrient deficiencies, anaemia and hypoproteinaemia. Increased lipopolysaccharide (LPS) permeability, stimulating the inflammatory response and resulting in chronic inflammation, has been identified as the leading cause of microbial overgrowth in the gut. The subject literature is extensive but of limited quality. Despite the recent interest in the gut microbiome and its disorders, more clinical research is needed to determine the pathophysiology, effective treatments, and prevention of small and large intestinal microbiota overgrowth. This review was designed to provide an overview of the available literature on intestinal microbial dysbiosis (SIBO, LIBO, SIFO and IMO) and to determine whether it represents a real threat to human health.
Collapse
Affiliation(s)
- Michalina Banaszak
- Department of Bromatology, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland
- Poznan University of Medical Sciences Doctoral School, Poznan University of Medical Sciences, Bukowska 70, 60-812 Poznan, Poland
| | - Ilona Górna
- Department of Bromatology, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland
| | - Dagmara Woźniak
- Department of Bromatology, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland
- Poznan University of Medical Sciences Doctoral School, Poznan University of Medical Sciences, Bukowska 70, 60-812 Poznan, Poland
| | - Juliusz Przysławski
- Department of Bromatology, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland
| | - Sławomira Drzymała-Czyż
- Department of Bromatology, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland
| |
Collapse
|
27
|
Quaye EK, Adjei RL, Isawumi A, Allen DJ, Caporaso JG, Quaye O. Altered Faecal Microbiota Composition and Structure of Ghanaian Children with Acute Gastroenteritis. Int J Mol Sci 2023; 24:3607. [PMID: 36835017 PMCID: PMC9962333 DOI: 10.3390/ijms24043607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Acute gastroenteritis (AGE) is a disease of global public health importance. Recent studies show that children with AGE have an altered gut microbiota relative to non-AGE controls. Yet, how the gut microbiota differs in Ghanaian children with and without AGE remains unclear. Here, we explore the 16S rRNA gene-based faecal microbiota profiles of Ghanaian children five years of age and younger, comprising 57 AGE cases and 50 healthy controls. We found that AGE cases were associated with lower microbial diversity and altered microbial sequence profiles relative to the controls. The faecal microbiota of AGE cases was enriched for disease-associated bacterial genera, including Enterococcus, Streptococcus, and Staphylococcus. In contrast, the faecal microbiota of controls was enriched for potentially beneficial genera, including Faecalibacterium, Prevotella, Ruminococcus, and Bacteroides. Lastly, distinct microbial correlation network characteristics were observed between AGE cases and controls, thereby supporting broad differences in faecal microbiota structure. Altogether, we show that the faecal microbiota of Ghanaian children with AGE differ from controls and are enriched for bacterial genera increasingly associated with diseases.
Collapse
Affiliation(s)
- Emmanuel Kofi Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Raymond Lovelace Adjei
- Council for Scientific and Industrial Research (CSIR)-Animal Research Institute, Accra P.O. Box AH 20, Ghana
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - David J. Allen
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - J. Gregory Caporaso
- Centre for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra P.O. Box LG 54, Ghana
| |
Collapse
|
28
|
Bao S, Wang H, Li W, Wu H, Lu C, Yong L, Zhang Q, Lu X, Zhao M, Lu J, Liu J, Ikechukwu CK, Xu J, Ni P, Xiong Y, Zhang W, Zhou C. Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection. Gut Microbes 2023; 15:2234653. [PMID: 37448101 PMCID: PMC10351451 DOI: 10.1080/19490976.2023.2234653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/25/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae. Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales. The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.
Collapse
Affiliation(s)
- Siwen Bao
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai’an Hospital of Xuzhou Medical University, Huai’an, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, China
| | - Chunying Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Liang Yong
- Department of Clinical Laboratory, The Affiliated Huai’an Hospital of Xuzhou Medical University, Huai’an, China
| | - Qing Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jia Liu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, China
| | | | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Ying Xiong
- Department of Pharmacy, Yancheng Third People’s Hospital, Yancheng, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| |
Collapse
|
29
|
A self-powered ingestible wireless biosensing system for real-time in situ monitoring of gastrointestinal tract metabolites. Nat Commun 2022; 13:7405. [PMID: 36456568 PMCID: PMC9715945 DOI: 10.1038/s41467-022-35074-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Information related to the diverse and dynamic metabolite composition of the small intestine is crucial for the diagnosis and treatment of various diseases. However, our current understanding of the physiochemical dynamics of metabolic processes within the small intestine is limited due to the lack of in situ access to the intestinal environment. Here, we report a demonstration of a battery-free ingestible biosensing system for monitoring metabolites in the small intestine. As a proof of concept, we monitor the intestinal glucose dynamics on a porcine model. Battery-free operation is achieved through a self-powered glucose biofuel cell/biosensor integrated into a circuit that performs energy harvesting, biosensing, and wireless telemetry via a power-to-frequency conversion scheme using magnetic human body communication. Such long-term biochemical analysis could potentially provide critical information regarding the complex and dynamic small intestine metabolic profiles.
Collapse
|
30
|
Sun J, Chen W, Yuan Z. Characterization of Intestinal Microbiota in Lambs with Different Susceptibility to Escherichia coli F17. Vet Sci 2022; 9:vetsci9120670. [PMID: 36548832 PMCID: PMC9782581 DOI: 10.3390/vetsci9120670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Diarrhea is one of the most commonly reported diseases in young farm animals. Escherichia coli (E. coli) F17 is one of the major pathogenic bacteria responsible for diarrhea. However, the pathogenicity of diarrhea in lambs involving E. coli F17 strains and how E. coli F17 infection modifies lambs' intestinal microbiota are largely unknown. To evaluate diarrhea in newborn lambs with an infection of E. coli F17, 50 lambs were selected for challenge experiments and divided into four groups, namely, a high-dose challenge group, low-dose challenge group, positive control group, and negative control group. The E. coli F17 challenge experiments caused diarrhea and increased mortality in the experimental lamb population, with a higher prevalence (90%), mortality (35%), and rapid onset time (4-12 h) being observed in the high-dose challenge group than the results observed in the low-dose challenge group (75%, 10%, 6-24 h, respectively). After the challenge experiment, healthy lambs in the high-dose challenge group and severely diarrheic lamb in the low-dose challenge group were identified as lambs sensitive/resistant to E. coli F17 (E. coli F17 -resistant/-sensitive candidate, AN/SE) according to the histopathological detection. Results of intestinal contents bacteria plate counting revealed that the number of bacteria in the intestinal contents of SE lambs was 102~3-fold greater than that of the AN lambs, especially in the jejunum. Then, 16S rRNA sequencing was conducted to profile the intestinal microbiota using the jejunal contents, and the results showed that SE lambs had higher Lactococcus and a lower Bacteroidetes:Firmicutes ratio and intestinal microbiota diversity in the jejunum than AN lambs. Notably, high abundance of Megasphaera elsdenii was revealed in AN lambs, which indicated that Megasphaera elsdenii may serve as a potential probiotic for E. coli F17 infection. Our study provides an alternative challenge model for the identification of E. coli F17-sensitive/-resistant lambs and contributes to the basic understandings of intestinal microbiota in lambs with different susceptibilities to E. coli F17.
Collapse
Affiliation(s)
- Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- Correspondence:
| |
Collapse
|
31
|
Multi-Time-Point Fecal Sampling in Human and Mouse Reveals the Formation of New Homeostasis in Gut Microbiota after Bowel Cleansing. Microorganisms 2022; 10:microorganisms10122317. [PMID: 36557570 PMCID: PMC9783159 DOI: 10.3390/microorganisms10122317] [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: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Polyethylene glycol (PEG) is one of the most commonly used bowel cleansing methods. Although the safety of PEG for bowel cleansing has been proven, its impact on intestinal microbiota has not been clearly explained, especially in terms of the dynamic changes in intestinal microbiota after PEG bowel cleansing, and there are no consistent results. In this study, stool samples were collected from 12 participants at six time points before and after bowel cleansing. We obtained data on the microbiota of these samples using 16S rRNA gene sequencing and analysis. The data revealed that the structure and composition of the microbiota changed greatly approximately 7 d after intestinal cleansing. The analysis of the dynamic changes in the microbiota showed that the change was most significant at day 3, but the internal structure of the microbiota was similar to that before bowel cleansing. A comparison of the most significantly changed microbiota at different time points before and after bowel cleansing revealed four bacteria: Bacteroides, Roseburia, Eubacterium, and Bifidobacterium. We also established a humanized mouse model to simulate human bowel cleansing using PEG. The results showed that the mouse model achieved similar effects to human bowel cleansing, but its recovery speed was one stage earlier than that of humans. These findings suggest that the intestinal microbiota after bowel cleansing initially underwent a short-term change and then actively returned to its initial status. The results on key bacteria and establishment of mouse models can provide a reference for subsequent research on bowel cleansing.
Collapse
|
32
|
Zhong T, Wang Y, Wang X, Freitas-de-Melo A, Li H, Zhan S, Wang L, Cao J, Dai D, Guo J, Li L, Zhang H, Liu J, Niu L. Diarrhea in suckling lambs is associated with changes in gut microbiota, serum immunological and biochemical parameters in an intensive production system. Front Microbiol 2022; 13:1020657. [PMID: 36466638 PMCID: PMC9712182 DOI: 10.3389/fmicb.2022.1020657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
The incidence of diarrhea in lambs is frequent in large-scale sheep farms, which greatly impacts the growth and health of lambs. The aim of this study was to assess the changes in serum biochemical and immunological parameters and gut microbiome composition in suckling lambs suffering from diarrhea or not, reared on an intensive commercial farm. We found a reduced diversity of intestinal bacteria in suckling lambs suffering from diarrhea. Firmicutes and Bacteroidetes were the dominant flora in both groups of lambs, while the Bacteroidetes decreased in diarrheic lambs, no changes were reported in Firmicutes. Compared with healthy lambs, the proportion of aerobic bacteria, facultative anaerobic bacteria, and stress tolerant bacteria increased in lambs suffering from diarrhea, while that of anaerobic bacteria and potentially pathogenic bacteria decreased slightly. In addition, the contents of total cholesterol, immunoglobulins (Ig) G, and IgM in the serum of lambs suffering from diarrhea were lower than those of healthy lambs. This study explored the association between diarrhea occurrence, intestinal microbial community structure, and metabolic and immunological status in Hu lambs.
Collapse
Affiliation(s)
- Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yaxuan Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinlu Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Aline Freitas-de-Melo
- Departamento de Biociencias Veterinarias, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Hua Li
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Dinghui Dai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinwang Liu
- Yulin Sannong Breeding Service Co., Ltd, Yulin, China
| | - Lili Niu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
33
|
Metagenomic analysis of diarrheal stools in Kolkata, India, indicates the possibility of subclinical infection of Vibrio cholerae O1. Sci Rep 2022; 12:19473. [PMID: 36376441 PMCID: PMC9663449 DOI: 10.1038/s41598-022-24167-9] [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: 10/22/2021] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
We examined the stools of 23 patients in Kolkata, who were diagnosed as cholera patients because Vibrio cholerae O1 was detected from their stools by culturing methods, and further explored by metagenomic sequencing analysis. Subsequently, the presence of the gene encoding A subunit of cholera toxin (ctxA) and the cholera toxin (CT) level in these stool samples were examined. ctxA was examined by both metagenomic sequencing analysis and polymerase chain reaction. In these examinations, two samples did not show positive in any of these tests. The metagenomic analysis showed that the genes for Streptococcus pneumoniae and Salmonella enterica were present in the stools of these two patients, respectively. Therefore, these two patients were not considered to have diarrhea due to V. cholerae infection. From these results, we predicted that some Kolkata residents harbor a small number of V. cholerae in their intestines as a form of subclinical infection with V. cholerae. Next, we analyzed the stool samples of 22 diarrhea patients from which V. cholerae was not isolated. The results showed that 3 of the patients seemed to have subclinical infection of V. cholerae based on the amount of the genes. These results indicated that subclinical infections with V. cholerae O1 occur in Kolkata.
Collapse
|
34
|
Ndungo E, Holm JB, Gama S, Buchwald AG, Tennant SM, Laufer MK, Pasetti MF, Rasko DA. Dynamics of the Gut Microbiome in Shigella-Infected Children during the First Two Years of Life. mSystems 2022; 7:e0044222. [PMID: 36121169 PMCID: PMC9600951 DOI: 10.1128/msystems.00442-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 02/02/2023] Open
Abstract
Shigella continues to be a major contributor to diarrheal illness and dysentery in children younger than 5 years of age in low- and middle-income countries. Strategies for the prevention of shigellosis have focused on enhancing adaptive immunity. The interaction between Shigella and intrinsic host factors, such as the microbiome, remains unknown. We hypothesized that Shigella infection would impact the developing microbial community in infancy and, conversely, that changes in the gastrointestinal microbiome may predispose infections. To test this hypothesis, we characterized the gastrointestinal microbiota in a longitudinal birth cohort from Malawi that was monitored for Shigella infection using 16S rRNA amplicon sequencing. Children with at least one Shigella quantitative polymerase chain reaction (qPCR) positive sample during the first 2 years of life (cases) were compared to uninfected controls that were matched for sex and age. Overall, the microbial species diversity, as measured by the Shannon diversity index, increased over time, regardless of case status. At early time points, the microbial community was dominated by Bifidobacterium longum and Escherichia/Shigella. A greater abundance of Prevotella 9 and Bifidobacterium kashiwanohense was observed at 2 years of age. While no single species was associated with susceptibility to Shigella infection, significant increases in Lachnospiraceae NK4A136 and Fusicatenibacter saccharivorans were observed following Shigella infection. Both taxa are in the family Lachnospiraceae, which are known short-chain fatty acid producers that may improve gut health. Our findings identified temporal changes in the gastrointestinal microbiota associated with Shigella infection in Malawian children and highlight the need to further elucidate the microbial communities associated with disease susceptibility and resolution. IMPORTANCE Shigella causes more than 180 million cases of diarrhea globally, mostly in children living in poor regions. Infection can lead to severe health impairments that reduce quality of life. There is increasing evidence that disruptions in the gut microbiome early in life can influence susceptibility to illnesses. A delayed or impaired reconstitution of the microbiota following infection can further impact overall health. Aiming to improve our understanding of the interaction between Shigella and the developing infant microbiome, we investigated changes in the gut microbiome of Shigella-infected and uninfected children over the course of their first 2 years of life. We identified species that may be involved in recovery from Shigella infection and in driving the microbiota back to homeostasis. These findings support future studies into the elucidation of the interaction between the microbiota and enteric pathogens in young children and into the identification of potential targets for prevention or treatment.
Collapse
Affiliation(s)
- Esther Ndungo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Johanna B. Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Syze Gama
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Andrea G. Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sharon M. Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
35
|
Mosca A, Abreu Y Abreu AT, Gwee KA, Ianiro G, Tack J, Nguyen TVH, Hill C. The clinical evidence for postbiotics as microbial therapeutics. Gut Microbes 2022; 14:2117508. [PMID: 36184735 PMCID: PMC9542959 DOI: 10.1080/19490976.2022.2117508] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
An optimally operating microbiome supports protective, metabolic, and immune functions, but disruptions produce metabolites and toxins which can be involved in many conditions. Probiotics have the potential to manage these. However, their use in vulnerable people is linked to possible safety concerns and maintaining their viability is difficult. Interest in postbiotics is therefore increasing. Postbiotics contain inactivated microbial cells or cell components, thus are more stable and exert similar health benefits to probiotics. To review the evidence for the clinical benefits of postbiotics in highly prevalent conditions and consider future potential areas of benefit. There is growing evidence revealing the diverse clinical benefits of postbiotics in many prevalent conditions. Postbiotics could offer a novel therapeutic approach and may be a safer alternative to probiotics. Establishing interaction mechanisms between postbiotics and commensal microorganisms will improve the understanding of potential clinical benefits and may lead to targeted postbiotic therapy.
Collapse
Affiliation(s)
- Alexis Mosca
- Pediatric Gastroenterology and Nutrition Department, APHP Robert Debré, Paris, France
| | - Ana Teresa Abreu Y Abreu
- Gastroenterologist and Neuro-gastroenterologist, Angeles del Pedregal Hospital, Mexico City, Mexico
| | - Kok Ann Gwee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and Gleneagles Hospital, Singapore
| | - Gianluca Ianiro
- Gastroenterology Unit, Fondazione Policlinico Universitario”A. Gemelli” IRCCS, Rome, Italy
| | - Jan Tack
- Department of Gastroenterology, University Hospitals Leuven, Belgium
| | | | - Colin Hill
- APC Microbiome Institute, University College Cork, Ireland,CONTACT Prof. Colin HILL APC Microbiome Institute, University College Cork, Ireland
| |
Collapse
|
36
|
Ren W, Yu B, Yu J, Zheng P, Huang Z, Luo J, Mao X, He J, Yan H, Wu J, Chen D, Luo Y. Lower abundance of Bacteroides and metabolic dysfunction are highly associated with the post-weaning diarrhea in piglets. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2062-2075. [PMID: 35467318 DOI: 10.1007/s11427-021-2068-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Growing evidences show a direct link between diarrhea and disorders of gut microbiota in pigs. However, whether there are microbial markers associated with post-weaning diarrhea remains unknown. In the current study, we compared the microbial community, functions and metabolites between healthy weaned piglets (group H, n=7) and piglets with post-weaning diarrhea (group D, n=7), in order to find out diarrhea associated microbial markers. Each of 7 fecal samples was collected from H and D piglets (weaned at 21 d and sampled at 26 d). The metagenomic and untargeted metabolomic analysis revealed that the microbial composition, function and metabolic profile in D pigs was considerably reshaped, including the reduced abundance and number of Bacteroides, which significantly correlated with the diarrhea status of host. The carbohydrate metabolism, biosynthesis and metabolism, lipid metabolism, amino acid metabolism, and the activity of glycan and carbohydrates digestion related enzymes showed extensively down-regulated in D pigs compared with H pigs. Diarrhea significantly changed the metabolic profiles of fecal microbiota, and most of the altered metabolites were negatively or positively correlated with the change in the abundance of Bacteroides. In conclusion, the lower abundance of Bacteroides and its associated metabolic dysfunction may be regarded as microbial markers of physiological post-weaning diarrhea in piglets.
Collapse
Affiliation(s)
- Wen Ren
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- DSM (China) Animal Nutrition Research Center Co., Ltd, Bazhou, 065799, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yan
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinlong Wu
- DSM (China) Animal Nutrition Research Center Co., Ltd, Bazhou, 065799, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
37
|
Xia B, Zhong R, Wu W, Luo C, Meng Q, Gao Q, Zhao Y, Chen L, Zhang S, Zhao X, Zhang H. Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model. MICROBIOME 2022; 10:139. [PMID: 36045454 PMCID: PMC9429786 DOI: 10.1186/s40168-022-01326-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Post-weaning diarrhea in piglets reduces growth performance and increases mortality, thereby causing serious economic losses. The intestinal epithelial cells and microbiota reciprocally regulate each other in order to maintain intestinal homeostasis and control inflammation. However, a relative paucity of research has been focused on the host-derived regulatory network that controls mucin O-glycans and thereby changes gut microbiota during diarrhea in infancy. At the development stage just after birth, the ontogeny of intestinal epithelium, immune system, and gut microbiota appear similar in piglets and human infants. Here, we investigated the changes of mucin O-glycans associated with gut microbiota using a diarrheal post-weaned piglet model. RESULTS We found that diarrhea disrupted the colonic mucus layer and caused aberrant mucin O-glycans, including reduced acidic glycans and truncated glycans, leading to an impaired gut microenvironment. Subsequently, the onset of diarrhea, changes in microbiota and bacterial translocation, resulting in compromised epithelial barrier integrity, enhanced susceptibility to inflammation, and mild growth faltering. Furthermore, we found the activation of NLRP3 inflammasome complexes in the diarrheal piglets when compared to the healthy counterparts, triggered the release of proinflammatory cytokines IL-1β and IL-18, and diminished autophagosome formation, specifically the defective conversion of LC3A/B I into LC3A/B II and the accumulation of p62. Additionally, selective blocking of the autophagy pathway by 3-MA led to the reduction in goblet cell-specific gene transcript levels in vitro. CONCLUSIONS We observed that diarrheal piglets exhibited colonic microbiota dysbiosis and mucosal barrier dysfunction. Our data demonstrated that diarrhea resulted in the activation of inflammasomes and autophagy restriction along with aberrant mucin O-glycans including reduced acidic glycans and truncated glycans. The results suggested the mucin O-glycans-microbiota axis is likely associated with diarrheal pathogenesis. Our study provides novel insights into the pathophysiology of early-weaning-induced diarrheal disease in piglets and potentially understanding of disease mechanisms of diarrhea for human infants. Understanding the molecular pathology and pathogenesis of diarrhea is a prerequisite for the development of novel and effective therapies. Our data suggest that facilitating O-glycan elongation, modifying the microbiota, and developing specific inhibitors to some key inflammasomes could be the options for therapy of diarrhea including human infants. Video abstract.
Collapse
Affiliation(s)
- Bing Xia
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206 China
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Chengzeng Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qingtao Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Yong Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853 USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Quebec H9X3V9 Canada
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| |
Collapse
|
38
|
Kim M, Rodriguez-R LM, Hatt JK, Kayali O, Nalá R, Dunlop AL, Brennan PA, Corwin E, Smith AK, Brown J, Konstantinidis KT. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling. ISME COMMUNICATIONS 2022; 2:74. [PMID: 37938667 PMCID: PMC9723681 DOI: 10.1038/s43705-022-00154-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 07/05/2023]
Abstract
The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.
Collapse
Affiliation(s)
- Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80523, USA
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, 6020, Innsbruck, Tyrol, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Osman Kayali
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Rassul Nalá
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, 30332, USA
| | | | - Elizabeth Corwin
- School of Nursing, Columbia University, New York, NY, 10032, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North, Carolina, NC, 27599, USA.
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| |
Collapse
|
39
|
Izquierdo M, Lopez J, Gallardo P, Vidal RM, Ossa JC, Farfan MJ. Bacteria from gut microbiota associated with diarrheal infections in children promote virulence of Shiga toxin-producing and enteroaggregative Escherichia coli pathotypes. Front Cell Infect Microbiol 2022; 12:867205. [PMID: 36017363 PMCID: PMC9396624 DOI: 10.3389/fcimb.2022.867205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Diarrheagenic E. coli (DEC) pathogenicity relies on the interaction of bacteria with the host’s gut environment, which is regulated by the resident microbiota. Previously, we identified indicative bacterial species of gut microbiota in DEC-positive stool samples from children. Here, we evaluated the role of two indicative species, Citrobacter werkmanii (CW) and Escherichia albertii (EA), in the virulence of two DEC pathotypes, Shiga toxin-producing (STEC) and enteroaggregative (EAEC) Escherichia coli. Methods We determined the effect of supernatants obtained from CW and EA cultures on the gene expression of STEC strain 86-24 and EAEC strain 042 by RNA-seq analysis. We evaluated IL-8 secretion from T84 cells infected with these DEC strains in the presence or absence of the supernatant from EA. The effect of the supernatant from EA on the growth and adherence of STEC and EAEC to cells was also evaluated. Finally, we studied the effect of the EA supernatant on the STEC-induced inflammation mediated by the long polar fimbriae (Lpf) in T84 cells and the expression of plasmid-encoded toxin (Pet) in EAEC. Results RNA-seq analysis revealed that several virulence factors in STEC and EAEC were upregulated in the presence of supernatants from CW and EA. Interestingly, an increase in the secretion of IL-8 was observed in cells infected with STEC or EAEC in the presence of a supernatant from EA. Similar results were observed with the supernatants obtained from clinical strains of E. albertii. The supernatant from EA had no effect on the growth of STEC and EAEC, or on the ability of these DEC strains to adhere to cells. We found that Pet toxin in EAEC was upregulated in the presence of a supernatant from EA. In STEC, using mutant strains for Lpf fimbriae, our data suggested that these fimbriae might be participating in the increase in IL-8 induced by STEC in cells in the presence of a supernatant from EA. Conclusion Supernatant obtained from an indicative species of DEC-positive diarrhea could modulate gene expression in STEC and EAEC, and IL-8 secretion induced by these bacteria. These data provide new insights into the effect of gut microbiota species in the pathogenicity of STEC and EAEC.
Collapse
Affiliation(s)
- Mariana Izquierdo
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Joaquín Lopez
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Pablo Gallardo
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto M. Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juan C. Ossa
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio J. Farfan
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- *Correspondence: Mauricio J. Farfan,
| |
Collapse
|
40
|
Kumar MS, Slud EV, Hehnly C, Zhang L, Broach J, Irizarry RA, Schiff SJ, Paulson JN. Differential richness inference for 16S rRNA marker gene surveys. Genome Biol 2022; 23:166. [PMID: 35915508 PMCID: PMC9344657 DOI: 10.1186/s13059-022-02722-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is essential. While microbiome data generated using high-throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa. RESULTS When this artificial inflation in the observed number of taxa is ignored, we find that changes in the abundance of detected taxa confound current methods for inferring differences in richness. Experimental evidence, theory-guided exploratory data analyses, and existing literature support the conclusion that most sub-genus discoveries are spurious artifacts of clustering 16S sequencing reads. We proceed to model a 16S survey's systematic patterns of sub-genus taxa generation as a function of genus abundance to derive a robust control for false taxa accumulation. These controls unlock classical regression approaches for highly flexible differential richness inference at various levels of the surveyed microbial assemblage: from sample groups to specific taxa collections. The proposed methodology for differential richness inference is available through an R package, Prokounter. CONCLUSIONS False species discoveries bias richness estimation and confound differential richness inference. In the case of 16S microbiome surveys, supporting evidence indicate that most sub-genus taxa are spurious. Based on this finding, a flexible method is proposed and is shown to overcome the confounding problem noted with current approaches for differential richness inference. Package availability: https://github.com/mskb01/prokounter.
Collapse
Affiliation(s)
- M Senthil Kumar
- Department of Data Science, The Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Eric V Slud
- Department of Mathematics, University of Maryland, College Park, MD, USA
- Center for Statistical Research and Methodology U.S. Census Bureau, Suitland, MD, USA
| | - Christine Hehnly
- Penn State Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lijun Zhang
- Penn State Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - James Broach
- Penn State Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Rafael A Irizarry
- Department of Data Science, The Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Steven J Schiff
- Department of Neurosurgery, Yale University, New Haven, CT, 06510, USA
| | - Joseph N Paulson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Department of Data Sciences, Product Development, Genentech, South San Francisco, CA, USA.
| |
Collapse
|
41
|
Biazzo M, Deidda G. Fecal Microbiota Transplantation as New Therapeutic Avenue for Human Diseases. J Clin Med 2022; 11:jcm11144119. [PMID: 35887883 PMCID: PMC9320118 DOI: 10.3390/jcm11144119] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
The human body is home to a variety of micro-organisms. Most of these microbial communities reside in the gut and are referred to as gut microbiota. Over the last decades, compelling evidence showed that a number of human pathologies are associated with microbiota dysbiosis, thereby suggesting that the reinstatement of physiological microflora balance and composition might ameliorate the clinical symptoms. Among possible microbiota-targeted interventions, pre/pro-biotics supplementations were shown to provide effective results, but the main limitation remains in the limited microbial species available as probiotics. Differently, fecal microbiota transplantation involves the transplantation of a solution of fecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient's gut microbial composition aiming to confer a health benefit. Firstly used in the 4th century in traditional Chinese medicine, nowadays, it has been exploited so far to treat recurrent Clostridioides difficile infections, but accumulating data coming from a number of clinical trials clearly indicate that fecal microbiota transplantation may also carry the therapeutic potential for a number of other conditions ranging from gastrointestinal to liver diseases, from cancer to inflammatory, infectious, autoimmune diseases and brain disorders, obesity, and metabolic syndrome. In this review, we will summarize the commonly used preparation and delivery methods, comprehensively review the evidence obtained in clinical trials in different human conditions and discuss the variability in the results and the pivotal importance of donor selection. The final aim is to stimulate discussion and open new therapeutic perspectives among experts in the use of fecal microbiota transplantation not only in Clostridioides difficile infection but as one of the first strategies to be used to ameliorate a number of human conditions.
Collapse
Affiliation(s)
- Manuele Biazzo
- The BioArte Limited, Life Sciences Park, Triq San Giljan, SGN 3000 San Gwann, Malta;
- SienabioACTIVE, University of Siena, Via Aldo Moro 1, 53100 Siena, Italy
| | - Gabriele Deidda
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padova, Italy
- Correspondence: ; Tel.: +39-049-827-6125
| |
Collapse
|
42
|
Moroishi Y, Gui J, Hoen AG, Morrison HG, Baker ER, Nadeau KC, Li H, Li Z, Madan JC, Karagas MR. The relationship between the gut microbiome and the risk of respiratory infections among newborns. COMMUNICATIONS MEDICINE 2022; 2:87. [PMID: 35847562 PMCID: PMC9283516 DOI: 10.1038/s43856-022-00152-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/27/2022] [Indexed: 12/15/2022] Open
Abstract
Background Emerging evidence points to a critical role of the developing gut microbiome in immune maturation and infant health; however, prospective studies are lacking. Methods We examined the occurrence of infections and associated symptoms during the first year of life in relation to the infant gut microbiome at six weeks of age using bacterial 16S rRNA V4-V5 gene sequencing (N = 465) and shotgun metagenomics (N = 185). We used generalized estimating equations to assess the associations between longitudinal outcomes and 16S alpha diversity and metagenomics species. Results Here we show higher infant gut microbiota alpha diversity was associated with an increased risk of infections or respiratory symptoms treated with a prescription medicine, and specifically upper respiratory tract infections. Among vaginally delivered infants, a higher alpha diversity was associated with an increased risk of all-cause wheezing treated with a prescription medicine and diarrhea involving a visit to a health care provider. Positive associations were specifically observed with Veillonella species among all deliveries and Haemophilus influenzae among cesarean-delivered infants. Conclusion Our findings suggest that intestinal microbial diversity and the relative abundance of key taxa in early infancy may influence susceptibility to respiratory infection, wheezing, and diarrhea.
Collapse
Affiliation(s)
- Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
| | - Emily R. Baker
- Department of Obstetrics and Gynecology, Dartmouth-Hitchcock Medical Center, Lebanon, NH USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Zhigang Li
- Department of Biostatistics, University of Florida, Gainesville, FL USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| |
Collapse
|
43
|
Wang K, Peng X, Yang A, Huang Y, Tan Y, Qian Y, Lv F, Si H. Effects of Diets With Different Protein Levels on Lipid Metabolism and Gut Microbes in the Host of Different Genders. Front Nutr 2022; 9:940217. [PMID: 35782952 PMCID: PMC9240812 DOI: 10.3389/fnut.2022.940217] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/30/2022] [Indexed: 12/21/2022] Open
Abstract
The purpose of this experiment was to investigate the effects of different protein levels on lipid metabolism and gut microbes in mice of different genders. A total of 60 mice (30 female and 30 male) were randomly assigned to six groups and fed female mice with low protein diet (FLP), basal protein diet (FBD), and high protein diet (FHP). Similarly, the male mice fed with low protein diet (MLP), basal protein diet (MBD), and high protein diet (MHP). The low protein diet contained 14% CP, the basal diet contained 20% CP, and the high protein diet contained 26% CP. The results of the study showed that both basal and high protein diets significantly reduced the perirenal adipose tissues (PEAT) index in male mice compared to low protein diet (p < 0.05). For the gut, the FHP significantly increased the relative gut weight compared to the FBD and FLP (p < 0.05). At the same time, the FHP also significantly increased the relative gut length compared with the FBD and FLP (p < 0.05). The MHP significantly increased TC concentration compared with the MLP (p < 0.05), and the MBD tended to increase TC concentration compared with the MLP in serum (p = 0.084). The histomorphology result of the jejunum and ileum showed that a low protein diet was beneficial to the digestion and absorption of nutrients in the small intestine of mice. While different protein levels had no effect on the total number of fecal microbial species in mice, different protein levels had a significant effect on certain fecal microbes in mice, the absolute abundance of Verrucomicrobia in the feces of male mice was significantly higher in both high and basal protein diets than in the low protein diet (p < 0.05). The high protein diet significantly reduced the absolute abundance of Patescibacteria in the feces of female mice compared to both the basal and low protein diets (p < 0.05). The absolute abundance of Patescibacteria in male feces was not affected by dietary protein levels (p > 0.05). Taken together, our results suggest that a low protein diet can alter fat deposition and lipid metabolism in mice, and that it benefited small intestinal epithelial structure and microbes.
Collapse
Affiliation(s)
- Kaijun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaomin Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Anqi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yiqin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yuxiao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yajing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Feifei Lv
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongbin Si
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- *Correspondence: Hongbin Si,
| |
Collapse
|
44
|
Saeed NK, Al-Beltagi M, Bediwy AS, El-Sawaf Y, Toema O. Gut microbiota in various childhood disorders: Implication and indications. World J Gastroenterol 2022; 28:1875-1901. [PMID: 35664966 PMCID: PMC9150060 DOI: 10.3748/wjg.v28.i18.1875] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/08/2022] [Accepted: 03/27/2022] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota has a significant role in gut development, maturation, and immune system differentiation. It exerts considerable effects on the child's physical and mental development. The gut microbiota composition and structure depend on many host and microbial factors. The host factors include age, genetic pool, general health, dietary factors, medication use, the intestine's pH, peristalsis, and transit time, mucus secretions, mucous immunoglobulin, and tissue oxidation-reduction potentials. The microbial factors include nutrient availability, bacterial cooperation or antagonism, and bacterial adhesion. Each part of the gut has its microbiota due to its specific characteristics. The gut microbiota interacts with different body parts, affecting the pathogenesis of many local and systemic diseases. Dysbiosis is a common finding in many childhood disorders such as autism, failure to thrive, nutritional disorders, coeliac disease, Necrotizing Enterocolitis, helicobacter pylori infection, functional gastrointestinal disorders of childhood, inflammatory bowel diseases, and many other gastrointestinal disorders. Dysbiosis is also observed in allergic conditions like atopic dermatitis, allergic rhinitis, and asthma. Dysbiosis can also impact the development and the progression of immune disorders and cardiac disorders, including heart failure. Probiotic supplements could provide some help in managing these disorders. However, we are still in need of more studies. In this narrative review, we will shed some light on the role of microbiota in the development and management of common childhood disorders.
Collapse
Affiliation(s)
- Nermin Kamal Saeed
- Medical Microbiology Section, Department of Pathology, Salmaniya Medical Complex, Ministry of Health, Manama 12, Bahrain
- Microbiology Section, Department of Pathology, Irish Royal College of Surgeon, Busaiteen 15503, Bahrain
| | - Mohammed Al-Beltagi
- Department of Pediatrics, University Medical Center, Arabian Gulf University, Dr. Sulaiman Al Habib Medical Group, Manama 26671, Bahrain
- Department of Pediatrics, Faculty of Medicine, Tanta University, Tanta 31511, Egypt
| | - Adel Salah Bediwy
- Department of Chest Disease, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
- Department of Pulmonology, University Medical Center, Arabian Gulf University, Dr. Sulaiman Al Habib Medical Group, Manama 26671, Bahrain
| | - Yasser El-Sawaf
- Department of Tropical Medicine, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
- Department of Gastroenterology, University Medical Center, Arabian Gulf University, Dr. Sulaiman Al-Habib Medical Group, Manama 26671, Bahrain
| | - Osama Toema
- Department of Pediatrics, Faculty of Medicine, Tanta University, Tanta 31511, Egypt
| |
Collapse
|
45
|
Nadimpalli ML, Lanza VF, Montealegre MC, Sultana S, Fuhrmeister ER, Worby CJ, Teichmann L, Caduff L, Swarthout JM, Crider YS, Earl AM, Brown J, Luby SP, Islam MA, Julian TR, Pickering AJ. Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children. Nat Microbiol 2022; 7:620-629. [PMID: 35422497 PMCID: PMC9249080 DOI: 10.1038/s41564-022-01101-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
Healthy development of the gut microbiome provides long-term health benefits. Children raised in countries with high infectious disease burdens are frequently exposed to diarrhoeal pathogens and antibiotics, which perturb gut microbiome assembly. A recent cluster-randomized trial leveraging >4,000 child observations in Dhaka, Bangladesh, found that automated water chlorination of shared taps effectively reduced child diarrhoea and antibiotic use. In this substudy, we leveraged stool samples collected from 130 children 1 year after chlorine doser installation to examine differences between treatment and control children's gut microbiota. Water chlorination was associated with increased abundance of several bacterial genera previously linked to improved gut health; however, we observed no effects on the overall richness or diversity of taxa. Several clinically relevant antibiotic resistance genes were relatively more abundant in the gut microbiome of treatment children, possibly due to increases in Enterobacteriaceae. While further studies on the long-term health impacts of drinking chlorinated water would be valuable, we conclude that access to chlorinated water did not substantially impact child gut microbiome development in this setting, supporting the use of chlorination to increase global access to safe drinking water.
Collapse
Affiliation(s)
- Maya L. Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain,Network Research Center for Infectious Diseases (CIBERINFEC), Spain
| | | | - Sonia Sultana
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Erica R. Fuhrmeister
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Colin J. Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Lisa Teichmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Yoshika S. Crider
- Energy and Resources Group, University of California Berkeley, Berkeley, CA, USA,King Center on Global Development, Stanford University, Stanford, CA, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen P. Luby
- Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Mohammad Aminul Islam
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland,Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Timothy R. Julian
- Network Research Center for Infectious Diseases (CIBERINFEC), Spain,Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Amy J. Pickering
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA,Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA,Blum Center for Developing Economies, University of California, Berkeley, CA, USA,Correspondence and requests for materials should be addressed to Dr. Amy Pickering () and Dr. Tim Julian ()
| |
Collapse
|
46
|
Dynamic of the human gut microbiome under infectious diarrhea. Curr Opin Microbiol 2022; 66:79-85. [PMID: 35121284 DOI: 10.1016/j.mib.2022.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 11/20/2022]
Abstract
Despite the widespread implementation of sanitation, immunization and appropriate treatment, infectious diarrheal diseases still inflict a great health burden to children living in low resource settings. Conventional microbiology research in diarrhea have focused on the pathogen's biology and pathogenesis, but initial enteric infections could trigger subsequent perturbations in the gut microbiome, leading to short-term or long-term health effects. Conversely, such pre-existing perturbations could render children more vulnerable to enteropathogen colonization and diarrhea. Recent advances in DNA sequencing and bioinformatic analyses have been integrated in well-designed clinical and epidemiological studies, which allow us to track how the gut microbiome changes from disease onset to recovery. Here, we aim to summarize the current understanding on the diarrheal gut microbiome, stratified into different disease stages. Furthermore, we discuss how such perturbations could have impacts beyond an acute diarrhea episode, specifically on the child's nutritional status and the facilitation of antimicrobial resistance.
Collapse
|
47
|
Rahman SU, Zhou K, Zhou S, Sun T, Mi R, Huang Y, Han X, Gong H, Chen Z. Curcumin mitigates Cryptosporidium parvum infection through modulation of gut microbiota and innate immune-related genes in immunosuppressed neonatal mice. Microb Pathog 2022; 164:105424. [PMID: 35092833 DOI: 10.1016/j.micpath.2022.105424] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 01/04/2023]
Abstract
Cryptosporidium parvum is a major cause of diarrheal disease in immature or weakened immune systems, mainly in infants and young children in resource-poor settings. Despite its high prevalence, fully effective and safe drugs for the treatment of C. parvum infections remain scarce, and there is no vaccine. Meanwhile, curcumin has shown protective effects against C. parvum infections. However, the mechanisms of action and relationship to the gut microbiota and innate immune responses are unclear. Immunosuppressed neonatal mice were infected with oocysts of C. parvum and either untreated or treated with a normal diet, curcumin or paromomycin. We found that curcumin stopped C. parvum oocysts shedding in the feces of infected immunosuppressed neonatal mice, prevented epithelial damage, and villi degeneration, as well as prevented recurrence of infection. Curcumin supplementation increased the relative abundance of Bacteroidetes and decreased the relative abundance of Firmicutes and Proteobacteria in mice infected with C. parvum as shown by 16S rRNA gene sequencing analysis. The relative abundance of Lactobacillus, Bacteroides, Akkermansia, Desulfovibrio, Prevotella, and Helicobacter was significantly associated with C. parvum infection inhibited by curcumin. Curcumin significantly (P < 0.01) suppressed IFN-γ and IL -18 gene expression levels in immunosuppressed neonatal C. parvum-infected mice. We demonstrate that the therapeutic effects curcumin are associated with alterations in the gut microbiota and innate immune-related genes, which may be linked to the anti-Cryptosporidium mechanisms of curcumin.
Collapse
Affiliation(s)
- Sajid Ur Rahman
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Keke Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - ShaSha Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Tiancong Sun
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Rongsheng Mi
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Yan Huang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiangan Han
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Haiyan Gong
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Zhaoguo Chen
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| |
Collapse
|
48
|
George S, Aguilera X, Gallardo P, Farfán M, Lucero Y, Torres JP, Vidal R, O'Ryan M. Bacterial Gut Microbiota and Infections During Early Childhood. Front Microbiol 2022; 12:793050. [PMID: 35069488 PMCID: PMC8767011 DOI: 10.3389/fmicb.2021.793050] [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] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota composition during the first years of life is variable, dynamic and influenced by both prenatal and postnatal factors, such as maternal antibiotics administered during labor, delivery mode, maternal diet, breastfeeding, and/or antibiotic consumption during infancy. Furthermore, the microbiota displays bidirectional interactions with infectious agents, either through direct microbiota-microorganism interactions or indirectly through various stimuli of the host immune system. Here we review these interactions during childhood until 5 years of life, focusing on bacterial microbiota, the most common gastrointestinal and respiratory infections and two well characterized gastrointestinal diseases related to dysbiosis (necrotizing enterocolitis and Clostridioides difficile infection). To date, most peer-reviewed studies on the bacterial microbiota in childhood have been cross-sectional and have reported patterns of gut dysbiosis during infections as compared to healthy controls; prospective studies suggest that most children progressively return to a "healthy microbiota status" following infection. Animal models and/or studies focusing on specific preventive and therapeutic interventions, such as probiotic administration and fecal transplantation, support the role of the bacterial gut microbiota in modulating both enteric and respiratory infections. A more in depth understanding of the mechanisms involved in the establishment and maintenance of the early bacterial microbiota, focusing on specific components of the microbiota-immunity-infectious agent axis is necessary in order to better define potential preventive or therapeutic tools against significant infections in children.
Collapse
Affiliation(s)
- Sergio George
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Ximena Aguilera
- School of Medicine, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Pablo Gallardo
- Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Farfán
- Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Yalda Lucero
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Roberto del Río Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Juan Pablo Torres
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Miguel O'Ryan
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, University of Chile, Santiago, Chile
| |
Collapse
|
49
|
Nearing JT, Douglas GM, Hayes MG, MacDonald J, Desai DK, Allward N, Jones CMA, Wright RJ, Dhanani AS, Comeau AM, Langille MGI. Microbiome differential abundance methods produce different results across 38 datasets. Nat Commun 2022; 13:342. [PMID: 35039521 PMCID: PMC8763921 DOI: 10.1038/s41467-022-28034-z] [Citation(s) in RCA: 272] [Impact Index Per Article: 136.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. Here, we compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups. We test for differences in amplicon sequence variants and operational taxonomic units (ASVs) between these groups. Our findings confirm that these tools identified drastically different numbers and sets of significant ASVs, and that results depend on data pre-processing. For many tools the number of features identified correlate with aspects of the data, such as sample size, sequencing depth, and effect size of community differences. ALDEx2 and ANCOM-II produce the most consistent results across studies and agree best with the intersect of results from different approaches. Nevertheless, we recommend that researchers should use a consensus approach based on multiple differential abundance methods to help ensure robust biological interpretations. Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups, and show ALDEx2 and ANCOM-II produce the most consistent results.
Collapse
Affiliation(s)
- Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Molly G Hayes
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada
| | - Jocelyn MacDonald
- Department of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Dhwani K Desai
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada
| | - Nicole Allward
- Department of Civil and Resource Engineering, Dalhousie University, Halifax, NS, Canada
| | - Casey M A Jones
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Robyn J Wright
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Akhilesh S Dhanani
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada
| | - André M Comeau
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada.,Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
50
|
Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
Collapse
Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
| |
Collapse
|