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Ortiz PS, Choudhury A, Kearney CM. Validation of gavage sampling as tool for longitudinal sampling of microbiota of the mouse gastric lumen. J Microbiol Methods 2024; 221:106939. [PMID: 38653334 DOI: 10.1016/j.mimet.2024.106939] [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: 02/09/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Fecal samples are commonly used for longitudinal studies of the gut lumen microbiome to track the course of response to infection or drug treatment, but no comparable method has been evaluated for longitudinal analysis of the gastric lumen microbiome in mice. Herein, a buffer flush of the stomach with a flexible gavage needle was used to collect gastric contents at one or several time points without harming the mouse. These samples were compared to samples collected by sacrifice and dissection of the mouse stomach. Microbiota from these samples were sequenced and evaluated in two ways: the composition of samples as measured by beta diversity and the richness of samples as measured by alpha diversity. Additionally, the effect of multiple sampling every two days on these metrics were studied. DNA was extracted from each of these samples and Illumina 16S rRNA gene sequencing was performed. RESULTS First, taxonomic richness of gavage and dissection samples was compared. A greater number of taxa was detected in gavage samples than in dissection samples. Second, taxonomic richness was analyzed over time. No significant difference in taxonomic richness was observed with repeated gavage flushes. Third, a comparison was made of the taxonomic composition of samples collected by gavage versus dissection followed by a comparison of samples collected over multiple samplings. Nonmetric multidimensional scaling analysis revealed no clear differences between collection by gavage flushing or dissection. Using weighted Unifrac and Aitchison taxonomic distances between gavage and dissection samples were not significantly different from distances between gavage samples themselves, and no significant difference was found in the taxonomic composition of mice which were sampled repeatedly. Finally, relative abundances of specific identified taxa were compared, and eleven taxa were found to differ in frequency between collection methods. Using the more stringent Analysis of Composition of Microbiomes (ANCOM), seven was found to differ. Similarly, no significant differences were uncovered using these analyses over multiple samples by gastric flush. CONCLUSION In summary, the consistency of the microbiota collected by gastric flushing recommends its use for microbiome analysis of gastric fluid similar to the use of fecal sampling to study the gut lumen microbiome.
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Affiliation(s)
- Patrick S Ortiz
- Baylor University, Department of Biology, 101 Bagby Ave., Waco, TX 76706, USA
| | - Ankan Choudhury
- Baylor University, Department of Biology, 101 Bagby Ave., Waco, TX 76706, USA
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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Pereira H, Chakarov N, Hoffman JI, Rinaud T, Ottensmann M, Gladow KP, Tobias B, Caspers BA, Maraci Ö, Krüger O. Early-life factors shaping the gut microbiota of Common buzzard nestlings. Anim Microbiome 2024; 6:27. [PMID: 38745254 DOI: 10.1186/s42523-024-00313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors. RESULTS We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition. CONCLUSION Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Busche Tobias
- Medical School East Westphalia-Lippe & Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, NRW, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
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Ponda P, Cerise JE, Navetta-Modrov B, Kiehm J, Covelli GM, Weiss J, Lee AT. The age-specific microbiome of children with milk, egg, and peanut allergy. Ann Allergy Asthma Immunol 2024:S1081-1206(24)00276-X. [PMID: 38697287 DOI: 10.1016/j.anai.2024.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND Immune regulation by gut microbiota is affected by dysbiosis and may precede food allergy onset. Prior studies lacked comparisons stratified by age and clinical phenotype. OBJECTIVE To assess the microbiome of children with food allergy (<3 years, 3-18 years) compared with similar aged children without food allergy. METHODS A real-world prospective cross-sectional study performed from 2014 to 2019 recruited children highly likely to have milk, egg, or peanut allergy defined by history and serum IgE or confirmed by food challenge. 16S ribosomal RNA sequencing identified stool microbial DNA. Alpha and beta diversity was compared between groups with food allergy and healthy controls stratified by age. Differential abundance for non a priori taxa was accepted at absolute fold-change greater than 2 and q value less than 0.05. RESULTS A total of 70 patients were included (56 with food allergy and 14 healthy controls). Groups were not significantly different in age, gender at birth, race, mode of delivery, breastfeeding duration, or antibiotic exposure. Younger children with food allergy had similar alpha diversity compared with controls. Beta diversity was significantly different by age (P = .001). There was differential abundance of several a priori (P < .05) taxa (including Clostridia) only in younger children. Both a priori (including Coprococcus and Clostridia) and non a priori (q < 0.05) Acidobacteria_Gp15, Aestuariispira, Tindallia, and Desulfitispora were significant in older children with food allergy, especially with peanut allergy. CONCLUSION Dysbiosis associates with food allergy, most prominent in older children with peanut allergy. Younger children with and without food allergy have fewer differences in gut microbiota. This correlates with clinical observations of persistence of peanut allergy and improved efficacy and safety of oral immunotherapy in younger children. Age younger than 3 years should be considered when initiating therapeutic interventions.
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Affiliation(s)
- Punita Ponda
- Northwell, New Hyde Park, New York; Division of Allergy and Immunology, Cohen Children's Medical Center, New Hyde Park, New York.
| | - Jane E Cerise
- Biostatistics Unit, Office of Academic Affairs, Northwell Health, New Hyde Park, New York
| | - Brianne Navetta-Modrov
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, New York
| | - Jamie Kiehm
- Los Angeles County Department of Health Services, Los Angeles, California
| | - Grace M Covelli
- Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Jared Weiss
- Department of Psychiatry, New York University School of Medicine, New York, New York
| | - Annette T Lee
- Northwell, New Hyde Park, New York; Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York
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Baltazar-Díaz TA, Andrade-Villanueva JF, Sánchez-Álvarez P, Amador-Lara F, Holguín-Aguirre T, Sánchez-Reyes K, Álvarez-Zavala M, López-Roa RI, Bueno-Topete MR, González-Hernández LA. A Two-Faced Gut Microbiome: Butyrogenic and Proinflammatory Bacteria Predominate in the Intestinal Milieu of People Living with HIV from Western Mexico. Int J Mol Sci 2024; 25:4830. [PMID: 38732048 PMCID: PMC11084381 DOI: 10.3390/ijms25094830] [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: 02/29/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
HIV infection results in marked alterations in the gut microbiota (GM), such as the loss of microbial diversity and different taxonomic and metabolic profiles. Despite antiretroviral therapy (ART) partially ablating gastrointestinal alterations, the taxonomic profile after successful new ART has shown wide variations. Our objective was to determine the GM composition and functions in people living with HIV (PLWHIV) under ART in comparison to seronegative controls (SC). Fecal samples from 21 subjects (treated with integrase strand-transfer inhibitors, INSTIs) and 18 SC were included. We employed 16S rRNA amplicon sequencing, coupled with PICRUSt2 and fecal short-chain fatty acid (SCFA) quantification by gas chromatography. The INSTI group showed a decreased α-diversity (p < 0.001) compared to the SC group, at the expense of increased amounts of Pseudomonadota (Proteobacteria), Segatella copri, Lactobacillus, and Gram-negative bacteria. Concurrently, we observed an enrichment in Megasphaera and Butyricicoccus, both SCFA-producing bacteria, and significant elevations in fecal butyrate in this group (p < 0.001). Interestingly, gut dysbiosis in PLWHIV was characterized by a proinflammatory environment orchestrated by Pseudomonadota and elevated levels of butyrate associated with bacterial metabolic pathways, as well as the evident presence of butyrogenic bacteria. The role of this unique GM in PLWHIV should be evaluated, as well as the use of butyrate-based supplements and ART regimens that contain succinate, such as tenofovir disoproxil succinate. This mixed profile is described for the first time in PLWHIV from Mexico.
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Affiliation(s)
- Tonatiuh Abimael Baltazar-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Guadalajara 44340, Mexico;
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Jaime F. Andrade-Villanueva
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Paulina Sánchez-Álvarez
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Fernando Amador-Lara
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Tania Holguín-Aguirre
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Karina Sánchez-Reyes
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Monserrat Álvarez-Zavala
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Rocío Ivette López-Roa
- Laboratorio de Investigación y Desarrollo Farmacéutico, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Marcelino García Barragán 1421, Guadalajara 44430, Mexico;
| | - Miriam Ruth Bueno-Topete
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Guadalajara 44340, Mexico;
| | - Luz Alicia González-Hernández
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
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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.
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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
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Malloy E, Kates AE, Dixon J, Riley C, Safdar N, Hanson L. Vaginal and Rectal microbiome changes following administration of a multi-species antenatal probiotic: A randomized control trial. GUT MICROBES REPORTS 2024; 1:1-10. [PMID: 38708373 PMCID: PMC11065196 DOI: 10.1080/29933935.2024.2334311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/14/2024] [Indexed: 05/07/2024]
Abstract
The gut and vaginal microbiome undergo changes during pregnancy which may be protective or harmful to the birthing person. Probiotics have been found to cause protective changes to the gut and vaginal microbiomes, with the potential to improve perinatal outcomes. This randomized control trial compares the vaginal and rectal microbiomes before and after an antenatal probiotic or placebo intervention, with a diverse group of pregnant people and a special focus on racial disparities. The vaginal and rectal microbiomes reveal non-significant increased Lactobacillus in the probiotics group, with a greater increase in participants who identified as Black. Potential implications and future study are discussed.
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Affiliation(s)
- Emily Malloy
- Aurora UW Medical Group Midwifery & Wellness, Advocate Aurora Healthcare Milwaukee, USA
- College of Nursing, Marquette University, Milwaukee, USA
| | - Ashley E. Kates
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, Madison, USA
- William S. Middleton Memorial Veterans Hospital, Madison, USA
| | - Jonah Dixon
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, Madison, USA
- William S. Middleton Memorial Veterans Hospital, Madison, USA
| | - Colleen Riley
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, Madison, USA
- William S. Middleton Memorial Veterans Hospital, Madison, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, Madison, USA
- William S. Middleton Memorial Veterans Hospital, Madison, USA
| | - Lisa Hanson
- College of Nursing, Marquette University, Milwaukee, USA
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Wu KC, McCauley KE, Lynch SV, Nayak RR, King NJ, Patel S, Kim TY, Condra K, Fadrosh D, Nguyen D, Lin DL, Lynch K, Rogers SJ, Carter JT, Posselt AM, Stewart L, Schafer AL. Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy. J Bone Miner Res 2024; 39:95-105. [PMID: 38477719 DOI: 10.1093/jbmr/zjad017] [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: 04/21/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 03/14/2024]
Abstract
Laparoscopic sleeve gastrectomy (LSG), the most common bariatric surgical procedure, leads to durable weight loss and improves obesity-related comorbidities. However, it induces abnormalities in bone metabolism. One unexplored potential contributor is the gut microbiome, which influences bone metabolism and is altered after surgery. We characterized the relationship between the gut microbiome and skeletal health in severe obesity and after LSG. In a prospective cohort study, 23 adults with severe obesity underwent skeletal health assessment and stool collection preoperatively and 6 mo after LSG. Gut microbial diversity and composition were characterized using 16S rRNA gene sequencing, and fecal concentrations of short-chain fatty acids (SCFA) were measured with LC-MS/MS. Spearman's correlations and PERMANOVA analyses were applied to assess relationships between the gut microbiome and bone health measures including serum bone turnover markers (C-terminal telopeptide of type 1 collagen [CTx] and procollagen type 1 N-terminal propeptide [P1NP]), areal BMD, intestinal calcium absorption, and calciotropic hormones. Six months after LSG, CTx and P1NP increased (by median 188% and 61%, P < .01) and femoral neck BMD decreased (mean -3.3%, P < .01). Concurrently, there was a decrease in relative abundance of the phylum Firmicutes. Although there were no change in overall microbial diversity or fecal SCFA concentrations after LSG, those with greater within-subject change in gut community microbial composition (β-diversity) postoperatively had greater increases in P1NP level (ρ = 0.48, P = .02) and greater bone loss at the femoral neck (ρ = -0.43, P = .04). In addition, within-participant shifts in microbial richness/evenness (α-diversity) were associated with changes in IGF-1 levels (ρ = 0.56, P < .01). The lower the postoperative fecal butyrate concentration, the lower the IGF-1 level (ρ = 0.43, P = .04). Meanwhile, the larger the decrease in butyrate concentration, the higher the postoperative CTx (ρ = -0.43, P = .04). These findings suggest that LSG-induced gut microbiome alteration may influence skeletal outcomes postoperatively, and microbial influences on butyrate formation and IGF-1 are possible mechanisms.
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Affiliation(s)
- Karin C Wu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Kathryn E McCauley
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Renuka R Nayak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Nicole J King
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Sheena Patel
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, United States
| | - Tiffany Y Kim
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Katherine Condra
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Doug Fadrosh
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Dat Nguyen
- The Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Din L Lin
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Kole Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Stanley J Rogers
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Jonathan T Carter
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Andrew M Posselt
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Lygia Stewart
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
- Surgical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Anne L Schafer
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, United States
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9
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Luo M, Zhu J, Jia J, Zhang H, Zhao J. Progress on network modeling and analysis of gut microecology: a review. Appl Environ Microbiol 2024; 90:e0009224. [PMID: 38415584 PMCID: PMC11207142 DOI: 10.1128/aem.00092-24] [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] [Indexed: 02/29/2024] Open
Abstract
The gut microecological network is a complex microbial community within the human body that plays a key role in linking dietary nutrition and host physiology. To understand the complex relationships among microbes and their functions within this community, network analysis has emerged as a powerful tool. By representing the interactions between microbes and their associated omics data as a network, we can gain a comprehensive understanding of the ecological mechanisms that drive the human gut microbiota. In addition, the network-based approach provides a more intuitive analysis of the gut microbiota, simplifying the study of its complex dynamics and interdependencies. This review provides a comprehensive overview of the methods used to construct and analyze networks in the context of gut microecological background. We discuss various types of network modeling approaches, including co-occurrence networks, causal networks, dynamic networks, and multi-omics networks, and describe the analytical techniques used to identify important network properties. We also highlight the challenges and limitations of network modeling in this area, such as data scarcity and heterogeneity, and provide future research directions to overcome these limitations. By exploring these network-based methods, researchers can gain valuable insights into the intricate relationships and functional roles of microbial communities within the gut, ultimately advancing our understanding of the gut microbiota's impact on human health.
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Affiliation(s)
- Meng Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiajia Jia
- Key Laboratory of Advanced Process Control for Light Industry (Ministry of Education), Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
- Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
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10
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Lin H, Chen Y, Abror G, Price M, Morris A, Sun J, Palella F, Chew KW, Brown TT, Rinaldo CR, Peddada SD. The effect of sexual behavior on HIV-1 seroconversion is mediated by the gut microbiome and proinflammatory cytokines. RESEARCH SQUARE 2024:rs.3.rs-3868545. [PMID: 38343862 PMCID: PMC10854284 DOI: 10.21203/rs.3.rs-3868545/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The association between HIV-1 seroconversion and gut dysbiosis is well documented, and its association with sexual activity is also widely recognized. However, it is not known whether the gut dysbiosis mediates the effects of high-risk sexual behavior on HIV-1 seroconversion. In this report we focused on men who engaged in high-risk sexual behavior where they had receptive anal intercourse with multiple men. We demonstrate that proinflammatory cytokines, sCD14 and sCD163, and gut microbiota mediate the effects of this high-risk sexual behavior on subsequent HIV seroconversion. We discovered changes in the gut microbial ecology, prior to seroconversion, both in terms of the composition as well as inter-relationships among the commensal species. Furthermore, these changes correlate with future HIV seroconversion. Specifically, as the number of sexual partners increased, we discovered in a "dose-response" manner, a decrease in the abundance of commensal and short-chain fatty acid-producing species, A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp, and an increase in proinflammatory species Dehalobacterium spp. and Methanobrevibacter spp. These changes were also observed among subsequent HIV seroconverters. Interestingly, we also discovered a reduction in correlations among these commensal and short-chain fatty acid producing bacteria in a "dose-response" manner with the number of sexual partners. Our mediation analysis not only provides a conceptual model for the disease process but also provides clues for future clinical interventions that will manipulate the gut microbiota to treat high-risk subjects to prevent HIV seroconversion.
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Affiliation(s)
- Huang Lin
- Co-first authors
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC USA
| | - Yue Chen
- Co-first authors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Grace Abror
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA USA
| | - Meaghan Price
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Jing Sun
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Frank Palella
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Kara W Chew
- School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Todd T Brown
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Charles R Rinaldo
- Co-senior authors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Shyamal D Peddada
- Co-senior authors
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC USA
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11
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Parkin K, Palmer DJ, Verhasselt V, Amenyogbe N, Cooper MN, Christophersen CT, Prescott SL, Silva D, Martino D. Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants. Microorganisms 2024; 12:228. [PMID: 38276213 PMCID: PMC10819277 DOI: 10.3390/microorganisms12010228] [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: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Complementary feeding induces dramatic ecological shifts in the infant gut microbiota toward more diverse compositions and functional metabolic capacities, with potential implications for immune and metabolic health. The aim of this study was to examine whether the age at which solid foods are introduced differentially affects the microbiota in predominantly breastfed infants compared with predominantly formula-fed infants. We performed whole-genome shotgun metagenomic sequencing of infant stool samples from a cohort of six-month-old Australian infants enrolled in a nested study within the ORIGINS Project longitudinal birth cohort. Infants born preterm or those who had been administered antibiotics since birth were excluded. The taxonomic composition was highly variable among individuals at this age. Predominantly formula-fed infants exhibited a higher microbiome diversity than predominantly breastfed infants. Among the predominantly breastfed infants, the introduction of solid foods prior to five months of age was associated with higher alpha diversity than solid food introduction after six months of age, primarily due to the loss of Bifidobacterium infantis. In contrast, the age at which solid food was introduced was not associated with the overall change in diversity among predominantly formula-fed infants but was associated with compositional changes in Escherichia abundance. Examining the functional capacity of the microbiota in relation to these changes, we found that the introduction of solid foods after six months of age was associated with elevated one-carbon compound metabolic pathways in both breastfed and formula-fed infants, although the specific metabolic sub-pathways differed, likely reflecting different taxonomic compositions. Our findings suggest that the age of commencement of solid foods influences the gut microbiota composition differently in predominantly breastfed infants than in predominantly formula-fed infants.
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Affiliation(s)
- Kimberley Parkin
- Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia; (K.P.)
- Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Debra J. Palmer
- Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia; (K.P.)
- Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Valerie Verhasselt
- Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia; (K.P.)
- Larsson-Rosenquist Foundation Centre for Immunology and Breastfeeding, Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Nelly Amenyogbe
- Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia; (K.P.)
| | - Matthew N. Cooper
- Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia; (K.P.)
| | - Claus T. Christophersen
- School of Molecular Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
- School of Medical and Health Sciences, Edith Cowen University, Joondalup, Perth, WA 6027, Australia
| | - Susan L. Prescott
- Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia
- School of Molecular Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
- Joondalup Health Campus, Joondalup, Perth, WA 6027, Australia
- Nova Institute for Health, Baltimore, MD 21231, USA
- Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The ORIGINS Project, Telethon Kids Institute, Nedlands, Perth, WA 6009, Australia
| | - Desiree Silva
- Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia
- School of Molecular Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
- School of Medical and Health Sciences, Edith Cowen University, Joondalup, Perth, WA 6027, Australia
- Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The ORIGINS Project, Telethon Kids Institute, Nedlands, Perth, WA 6009, Australia
| | - David Martino
- Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia; (K.P.)
- School of Molecular Science, University of Western Australia, Nedlands, Perth, WA 6009, Australia
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12
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She JJ, Liu WX, Ding XM, Guo G, Han J, Shi FY, Lau HCH, Ding CG, Xue WJ, Shi W, Liu GX, Zhang Z, Hu CH, Chen Y, Wong CC, Yu J. Defining the biogeographical map and potential bacterial translocation of microbiome in human 'surface organs'. Nat Commun 2024; 15:427. [PMID: 38199995 PMCID: PMC10781665 DOI: 10.1038/s41467-024-44720-6] [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: 05/28/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
The microbiome in a specific human organ has been well-studied, but few reports have investigated the multi-organ microbiome as a whole. Here, we aim to analyse the intra-individual inter-organ and intra-organ microbiome in deceased humans. We collected 1608 samples from 53 sites of 7 surface organs (oral cavity, esophagus, stomach, small intestine, appendix, large intestine and skin; n = 33 subjects) and performed microbiome profiling, including 16S full-length sequencing. Microbial diversity varied dramatically among organs, and core microbial species co-existed in different intra-individual organs. We deciphered microbial changes across distinct intra-organ sites, and identified signature microbes, their functional traits, and interactions specific to each site. We revealed significant microbial heterogeneity between paired mucosa-lumen samples of stomach, small intestine, and large intestine. Finally, we established the landscape of inter-organ relationships of microbes along the digestive tract. Therefore, we generate a catalogue of bacterial composition, diversity, interaction, functional traits, and bacterial translocation in human at inter-organ and intra-organ levels.
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Affiliation(s)
- Jun-Jun She
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China.
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.
- Yulin Hospital, First Affiliated Hospital of Xi'an Jiao Tong University, Yulin, China.
| | - Wei-Xin Liu
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao-Ming Ding
- Department of Kidney Transplantation, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Institute of Organ Transplantation, Xi'an Jiao Tong University, Xi'an, China
| | - Gang Guo
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Jing Han
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Fei-Yu Shi
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chen-Guang Ding
- Department of Kidney Transplantation, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Institute of Organ Transplantation, Xi'an Jiao Tong University, Xi'an, China
| | - Wu-Jun Xue
- Department of Kidney Transplantation, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Institute of Organ Transplantation, Xi'an Jiao Tong University, Xi'an, China
| | - Wen Shi
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Gai-Xia Liu
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Zhe Zhang
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Chen-Hao Hu
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Yinnan Chen
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Chi Chun Wong
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China.
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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13
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Neal K, Amachawadi RG, White BJ, Shippy TD, Theurer ME, Larson RL, Lubbers BV, Kleinhenz M. Nasopharyngeal Bacterial Prevalence and Microbial Diversity at First Treatment for Bovine Respiratory Disease (BRD) and Its Associations with Health and Mortality Outcomes in Feedyard Cattle. Microorganisms 2023; 12:33. [PMID: 38257861 PMCID: PMC10818627 DOI: 10.3390/microorganisms12010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Bovine respiratory disease (BRD) is an economically important disease in feedyards influencing both animal welfare and antimicrobial utilization. Major pathogens associated with BRD have been identified in previous research, but little information is available on the relationship between nasopharyngeal microbiota and health outcomes. The objective of this study was to identify potential associations between nasopharyngeal microbiota and antimicrobial resistance patterns of clinical cases that lived or died compared to non-diseased controls. Enrolled animals were subdivided based on clinical disease status and case outcome (subsequent mortality). Deep nasopharyngeal swabs were collected on enrolled animals and submitted for bacterial isolation, antimicrobial susceptibility determination, and metagenomics analysis. Enrolled cattle were represented in three groups: animals at first treatment for BRD that subsequently died (BRDM, n = 9), animals at first treatment for BRD that subsequently lived (BRDL, n = 15), and animals that were never treated for BRD during the feeding phase (CONT, n = 11). Antimicrobial resistance patterns for Pasteurella multocida illustrated cattle in each outcome category had isolates that were pan-susceptible or only showed resistance to oxytetracycline. The relative abundance of species and genera illustrated few differences among the three outcomes. Higher alpha diversity was identified in BRDL compared to CONT at the species level, and both BRDL and BRDM showed increased alpha diversity compared to CONT at the general level. Overall, this work illustrated nasopharyngeal microbiota showed relatively few differences among BRD cases that lived or died compared to animals without BRD.
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Affiliation(s)
- Kyndall Neal
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Raghavendra G. Amachawadi
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Brad J. White
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Teresa D. Shippy
- Data Science Center, Division of Biology, Kansas State University, Manhattan, KS 66506, USA;
| | - Miles E. Theurer
- Veterinary Research and Consulting Services LLC, Hays, KS 67601, USA;
| | - Robert L. Larson
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Brian V. Lubbers
- Beef Cattle Institute, Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (K.N.); (B.J.W.); (R.L.L.); (B.V.L.)
| | - Michael Kleinhenz
- Veterinary Education, Research and Outreach, Texas A&M University, Canyon, TX 79015, USA;
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14
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Ward G, Wurster JI, Lamb PS, DeCost G, Belenky P, Monnig MA. Alcohol consumption and oral microbiome composition in a sample of healthy young adults. Alcohol Alcohol 2023; 58:573-577. [PMID: 37501505 PMCID: PMC10642607 DOI: 10.1093/alcalc/agad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Abstract
The oral microbiomes of 24 healthy adults (50% female; mean age = 24.3) were examined using 16 s ribosomal RNA sequencing and compared between light and heavy drinkers. Beta diversity was related at the trend level to drinking group, and light drinkers had significantly higher abundances of key oral taxa such as Lactobacillales. These preliminary results may offer insight into early effects of heavy drinking on the composition of the oral microbiome.
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Affiliation(s)
- Gyles Ward
- New York University Langone Health, New York, NY 10016, United States
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, United States
| | - Philip S Lamb
- Institute of Child Development, University of Minnesota, Minneapolis, MN 55455, United States
| | - Grace DeCost
- Center for Alcohol and Addiction Studies, Brown University School of Public Health, Providence, RI 02912, United States
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, United States
| | - Mollie A Monnig
- Center for Alcohol and Addiction Studies, Brown University School of Public Health, Providence, RI 02912, United States
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15
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Cauwenberghs E, Oerlemans E, Wittouck S, Allonsius CN, Gehrmann T, Ahannach S, De Boeck I, Spacova I, Bron PA, Donders G, Verhoeven V, Lebeer S. Salivary microbiome of healthy women of reproductive age. mBio 2023; 14:e0030023. [PMID: 37655878 PMCID: PMC10653790 DOI: 10.1128/mbio.00300-23] [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: 03/07/2023] [Accepted: 07/10/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE The salivary microbiome has been proven to play a crucial role in local and systemic diseases. Moreover, the effects of biological and lifestyle factors such as oral hygiene and smoking on this microbial community have already been explored. However, what was not yet well understood was the natural variation of the saliva microbiome in healthy women and how this is associated with specific use of hormonal contraception and with the number of different sexual partners with whom microbiome exchange is expected regularly. In this paper, we characterized the salivary microbiome of 255 healthy women of reproductive age using an in-depth questionnaire and self-sampling kits. Using the large metadata set, we were able to investigate the associations of several host-related and lifestyle variables with the salivary microbiome profiles. Our study shows a high preservation between individuals.
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Affiliation(s)
- Eline Cauwenberghs
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Eline Oerlemans
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Camille Nina Allonsius
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Thies Gehrmann
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Ilke De Boeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Peter A. Bron
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Gilbert Donders
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium
- Regional Hospital Heilig Hart, Tienen, Belgium
- Femicare, Clinical Research for Women, Tienen, Belgium
| | - Veronique Verhoeven
- Department of Family medicine and population health (FAMPOP), University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
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16
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Martinez-Porchas M, Preciado-Álvarez A, Vargas-Albores F, Gracia-Valenzuela MH, Cicala F, Martinez-Cordova LR, Medina-Félix D, Garibay-Valdez E. Microbiota plasticity in tilapia gut revealed by meta-analysis evaluating the effect of probiotics, prebiotics, and biofloc. PeerJ 2023; 11:e16213. [PMID: 37842054 PMCID: PMC10576497 DOI: 10.7717/peerj.16213] [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: 06/30/2023] [Accepted: 09/10/2023] [Indexed: 10/17/2023] Open
Abstract
Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia's gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances.
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Affiliation(s)
- Marcel Martinez-Porchas
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | - Aranza Preciado-Álvarez
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | - Francisco Vargas-Albores
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | | | - Francesco Cicala
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Province of Padua, Italy
| | | | - Diana Medina-Félix
- Departamento de Ecología, Universidad Estatal de Sonora, Hermosillo, Sonora, Mexico
| | - Estefania Garibay-Valdez
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
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Howe S, Kegley B, Powell J, Chen S, Zhao J. Effect of bovine respiratory disease on the respiratory microbiome: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1223090. [PMID: 37743862 PMCID: PMC10516580 DOI: 10.3389/fcimb.2023.1223090] [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: 05/15/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Bovine respiratory disease (BRD) is the most devastating disease affecting beef and dairy cattle producers in North America. An emerging area of interest is the respiratory microbiome's relationship with BRD. However, results regarding the effect of BRD on respiratory microbiome diversity are conflicting. Results To examine the effect of BRD on the alpha diversity of the respiratory microbiome, a meta-analysis analyzing the relationship between the standardized mean difference (SMD) of three alpha diversity metrics (Shannon's Diversity Index (Shannon), Chao1, and Observed features (OTUs, ASVs, species, and reads) and BRD was conducted. Our multi-level model found no difference in Chao1 and Observed features SMDs between calves with BRD and controls. The Shannon SMD was significantly greater in controls compared to that in calves with BRD. Furthermore, we re-analyzed 16S amplicon sequencing data from four previously published datasets to investigate BRD's effect on individual taxa abundances. Additionally, based on Bray Curtis and Jaccard distances, health status, sampling location, and dataset were all significant sources of variation. Using a consensus approach based on RandomForest, DESeq2, and ANCOM-BC2, we identified three differentially abundant amplicon sequence variants (ASVs) within the nasal cavity, ASV5_Mycoplasma, ASV19_Corynebacterium, and ASV37_Ruminococcaceae. However, no ASVs were differentially abundant in the other sampling locations. Moreover, based on SECOM analysis, ASV37_Ruminococcaceae had a negative relationship with ASV1_Mycoplasma_hyorhinis, ASV5_Mycoplasma, and ASV4_Mannheimia. ASV19_Corynebacterium had negative relationships with ASV1_Mycoplasma_hyorhinis, ASV4_Mannheimia, ASV54_Mycoplasma, ASV7_Mycoplasma, and ASV8_Pasteurella. Conclusions Our results confirm a relationship between bovine respiratory disease and respiratory microbiome diversity and composition, which provide additional insight into microbial community dynamics during BRD development. Furthermore, as sampling location and sample processing (dataset) can also affect results, consideration should be taken when comparing results across studies.
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Affiliation(s)
- Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Beth Kegley
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Jeremy Powell
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Shicheng Chen
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, United States
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
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López-García E, Benítez-Cabello A, Arenas-de Larriva AP, Gutierrez-Mariscal FM, Pérez-Martínez P, Yubero-Serrano EM, Arroyo-López FN, Garrido-Fernández A. Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight. Biomedicines 2023; 11:2134. [PMID: 37626632 PMCID: PMC10452682 DOI: 10.3390/biomedicines11082134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer's sex (male or female), age (19-46 years), and weight (48.6-99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers' age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota.
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Affiliation(s)
- Elio López-García
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
| | - Antonio Benítez-Cabello
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
| | - Antonio Pablo Arenas-de Larriva
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
| | - Francisco Miguel Gutierrez-Mariscal
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Pablo Pérez-Martínez
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Elena María Yubero-Serrano
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Francisco Noé Arroyo-López
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
| | - Antonio Garrido-Fernández
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
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Amit G, Bashan A. Top-down identification of keystone taxa in the microbiome. Nat Commun 2023; 14:3951. [PMID: 37402745 DOI: 10.1038/s41467-023-39459-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 06/14/2023] [Indexed: 07/06/2023] Open
Abstract
Keystone taxa in ecological communities are native taxa that play an especially important role in the stability of their ecosystem. However, we still lack an effective framework for identifying these taxa from the available high-throughput sequencing without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. In addition, while most microbial interaction models assume pair-wise relationships, it is yet unclear whether pair-wise interactions dominate the system, or whether higher-order interactions are relevant. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the taxa. Our method does not assume a priori knowledge of pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real high-throughput sequencing of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module - multiple candidate keystone species with correlated occurrence. The keystone analysis of single-time-point cross-sectional data is also later verified by the evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.
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Affiliation(s)
- Guy Amit
- Department of Physics, Bar-Ilan University, Ramat-Gan, 590002, Israel
- Department of Natural Sciences, The Open University of Israel, Raanana, 4353701, Israel
| | - Amir Bashan
- Department of Physics, Bar-Ilan University, Ramat-Gan, 590002, Israel.
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20
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Banzragch M, Sanli K, Stensvold CR, Kurt O, Ari S. Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease. Scand J Gastroenterol 2023; 58:1253-1263. [PMID: 37337895 DOI: 10.1080/00365521.2023.2223708] [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: 05/07/2023] [Revised: 05/27/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined. METHODS We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn's disease and ulcerative colitis. RESULTS The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients. CONCLUSIONS CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.
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Affiliation(s)
| | - Kemal Sanli
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
- Life Sciences, TUBITAK Marmara Research Center, Kocaeli, Turkey
| | - Christen Rune Stensvold
- Department of Microbiology and Infection Control, Statens Serum Institute, Copenhagen, Denmark
| | - Ozgur Kurt
- Department of Medical Microbiology, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
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