1
|
Cruells A, Cabrera-Rubio R, Bustamante M, Pelegrí D, Cirach M, Jimenez-Arenas P, Samarra A, Martínez-Costa C, Collado MC, Gascon M. The influence of pre- and postnatal exposure to air pollution and green spaces on infant's gut microbiota: Results from the MAMI birth cohort study. ENVIRONMENTAL RESEARCH 2024; 257:119283. [PMID: 38830395 DOI: 10.1016/j.envres.2024.119283] [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: 12/27/2023] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Animal and human studies indicate that exposure to air pollution and natural environments might modulate the gut microbiota, but epidemiological evidence is very scarce. OBJECTIVES To assess the potential impact of pre- and postnatal exposure to air pollution and green spaces on infant gut microbiota assembly and trajectories during the first year of life. METHODS MAMI ("MAternal MIcrobes") birth cohort (Valencia, Spain, N = 162) was used to study the impact of environmental exposure (acute and chronic) on infant gut microbiota during the first year of life (amplicon-based 16S rRNA sequencing). At 7 days and at 1, 6 and 12 months, residential pre- and postnatal exposure to air pollutants (NO2, black carbon -BC-, PM2.5 and O3) and green spaces indicators (NDVI and area of green spaces at 300, 500 and 1000 m buffers) were obtained. For the association between exposures and alpha diversity indicators linear regression models (cross-sectional analyses) and mixed models, including individual as a random effect (longitudinal analyses), were applied. For the differential taxon analysis, the ANCOM-BC package with a log count transformation and multiple-testing corrections were used. RESULTS Acute exposure in the first week of life and chronic postnatal exposure to NO2 were associated with a reduction in microbial alpha diversity, while the effects of green space exposure were not evident. Acute and chronic (prenatal or postnatal) exposure to NO2 resulted in increased abundance of Haemophilus, Akkermansia, Alistipes, Eggerthella, and Tyzerella populations, while increasing green space exposure associated with increased Negativicoccus, Senegalimassilia and Anaerococcus and decreased Tyzzerella and Lachnoclostridium populations. DISCUSSION We observed a decrease in the diversity of the gut microbiota and signs of alteration in its composition among infants exposed to higher levels of NO2. Increasing green space exposure was also associated with changes in gut microbial composition. Further research is needed to confirm these findings.
Collapse
Affiliation(s)
- Adrià Cruells
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Raúl Cabrera-Rubio
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Dolors Pelegrí
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Marta Cirach
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Pol Jimenez-Arenas
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, University of Valencia, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Mireia Gascon
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain.
| |
Collapse
|
2
|
Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S. Distinct gut microbiomes in Thai patients with colorectal polyps. World J Gastroenterol 2024; 30:3336-3355. [PMID: 39086748 PMCID: PMC11287419 DOI: 10.3748/wjg.v30.i27.3336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/30/2024] [Accepted: 05/31/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence [e.g., tubular adenoma (TA)] often progress to malignancy and are closely associated with changes in the composition of the gut microbiome. There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway, such as hyperplastic polyps (HP). Exploration of microbiome alterations associated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis. AIM To investigate gut microbiome signatures, microbial associations, and microbial functions in HP and TA patients. METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps [control group (CT), n = 40], patients with HP (n = 52), and patients with TA (n = 60). Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA. Analytical techniques in this study included differential abundance analysis, co-occurrence network analysis, and differential pathway analysis. RESULTS Colorectal cancer (CRC)-associated bacteria, including Streptococcus gallolyticus (S. gallolyticus), Bacteroides fragilis, and Clostridium symbiosum, were identified as characteristic microbial species in TA patients. Mediterraneibacter gnavus, associated with dysbiosis and gastrointestinal diseases, was significantly differentially abundant in the HP and TA groups. Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively, whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis (e.g., mevalonate); S. gallolyticus was a major contributor. Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients, whereas TA patients exhibited co-occurrence of CRC-associated bacteria. Furthermore, the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients. CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development, providing insights concerning the roles of microbial species, functional pathways, and microbial interactions in colorectal carcinogenesis.
Collapse
Affiliation(s)
- Thoranin Intarajak
- Bioinformatics Unit, Chulabhorn Royal Academy, Lak Si 10210, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | | | - Ahmad Nuruddin Khoiri
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Weerayuth Kittichotirat
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Chinae Thammarongtham
- National Center for Genetic Engineering and Biotechnology, King Mongkut's University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bank Khun Thian 10150, Bangkok, Thailand
- Fungal Biotechnology Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| |
Collapse
|
3
|
Wilde J, Slack E, Foster KR. Host control of the microbiome: Mechanisms, evolution, and disease. Science 2024; 385:eadi3338. [PMID: 39024451 DOI: 10.1126/science.adi3338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.
Collapse
Affiliation(s)
- Jacob Wilde
- Department of Biology, University of Oxford, Oxford, UK
| | - Emma Slack
- Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Basel Institute for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
4
|
Opron K, Begley LA, Erb-Downward JR, Li G, Alexis NE, Barjaktarevic I, Barr RG, Bleecker ER, Boucher R, Bowler RP, Christenson SA, Comellas AP, Criner G, Cooper CB, Couper D, Galban CJ, Han MK, Hastie A, Hatt C, Hoffman EA, Kaner RJ, Kesimer M, Krishnan JA, LaFon DC, Martinez FJ, Ortega VE, Peters SP, Paine R, Putcha N, Woodruff PG, Huffnagle GB, Kozik AJ, Curtis JL, Huang YJ. Loss of Airway Phylogenetic Diversity Is Associated with Clinical and Pathobiological Markers of Disease Development in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 210:186-200. [PMID: 38261629 PMCID: PMC11273318 DOI: 10.1164/rccm.202303-0489oc] [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: 03/15/2023] [Accepted: 01/23/2024] [Indexed: 01/25/2024] Open
Abstract
Rationale: The airway microbiome has the potential to shape chronic obstructive pulmonary disease (COPD) pathogenesis, but its relationship to outcomes in milder disease is unestablished. Objectives: To identify sputum microbiome characteristics associated with markers of COPD in participants of the Subpopulations and Intermediate Outcome Measures of COPD Study (SPIROMICS). Methods: Sputum DNA from 877 participants was analyzed using 16S ribosomal RNA gene sequencing. Relationships between baseline airway microbiota composition and clinical, radiographic, and mucoinflammatory markers, including longitudinal lung function trajectory, were examined. Measurements and Main Results: Participant data represented predominantly milder disease (Global Initiative for Chronic Obstructive Lung Disease stage 0-2 obstruction in 732 of 877 participants). Phylogenetic diversity (i.e., range of different species within a sample) correlated positively with baseline lung function, decreased with higher Global Initiative for Chronic Obstructive Lung Disease stage, and correlated negatively with symptom burden, radiographic markers of airway disease, and total mucin concentrations (P < 0.001). In covariate-adjusted regression models, organisms robustly associated with better lung function included Alloprevotella, Oribacterium, and Veillonella species. Conversely, lower lung function, greater symptoms, and radiographic measures of small airway disease were associated with enrichment in members of Streptococcus, Actinobacillus, Actinomyces, and other genera. Baseline sputum microbiota features were also associated with lung function trajectory during SPIROMICS follow-up (stable/improved, decline, or rapid decline groups). The stable/improved group (slope of FEV1 regression ⩾66th percentile) had greater bacterial diversity at baseline associated with enrichment in Prevotella, Leptotrichia, and Neisseria species. In contrast, the rapid decline group (FEV1 slope ⩽33rd percentile) had significantly lower baseline diversity associated with enrichment in Streptococcus species. Conclusions: In SPIROMICS, baseline airway microbiota features demonstrate divergent associations with better or worse COPD-related outcomes.
Collapse
Affiliation(s)
- Kristopher Opron
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Lesa A. Begley
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | | | - Gen Li
- Department of Biostatistics, School of Public Health
| | - Neil E. Alexis
- Center for Environmental Medicine, Asthma, and Lung Biology, Division of Allergy and Immunology
| | | | - R. Graham Barr
- Department of Medicine, Division of General Medicine and
- Department of Epidemiology, Columbia University Medical Center, New York, New York
| | | | - Richard Boucher
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Research Center, and
| | | | | | - Alejandro P. Comellas
- Department of Radiology
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | | | | | - David Couper
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - MeiLan K. Han
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Annette Hastie
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | - Eric A. Hoffman
- Department of Radiology
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Robert J. Kaner
- Weill Cornell, Division of Pulmonary and Critical Care Medicine, New York, New York
| | - Mehmet Kesimer
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Research Center, and
| | - Jerry A. Krishnan
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Breathe Chicago Center, University of Illinois Chicago, Chicago, Illinois
| | - David C. LaFon
- Division of Pulmonary, Allergy and Critical Care, University of Alabama at Birmingham, Alabama
| | - Fernando J. Martinez
- Weill Cornell, Division of Pulmonary and Critical Care Medicine, New York, New York
| | | | | | - Robert Paine
- Division of Respiratory, Critical Care, Occupational Pulmonary Medicine, University of Utah, Salt Lake City, Utah
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, Maryland; and
| | - Prescott G. Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Gary B. Huffnagle
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Molecular, Cellular and Developmental Biology and
| | - Ariangela J. Kozik
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Molecular, Cellular and Developmental Biology and
| | - Jeffrey L. Curtis
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Medical Service, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Yvonne J. Huang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
5
|
Karpinets TV, Mitani Y, Chang CC, Wu X, Song X, Flores II, McDaniel LK, Hoballah YM, Veguilla FJ, Ferrarotto R, Colbert LE, Ajami NJ, Jenq RR, Zhang J, Futreal AP, El-Naggar AK. Intratumoral microbiome of adenoid cystic carcinomas and comparison with other head and neck cancers. Sci Rep 2024; 14:16300. [PMID: 39009605 PMCID: PMC11251153 DOI: 10.1038/s41598-024-65939-9] [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: 03/26/2024] [Accepted: 06/25/2024] [Indexed: 07/17/2024] Open
Abstract
Adenoid cystic carcinoma (ACC) is a rare, usually slow-growing yet aggressive head and neck malignancy. Despite its clinical significance, our understanding of the cellular evolution and microenvironment in ACC remains limited. We investigated the intratumoral microbiomes of 50 ACC tumor tissues and 33 adjacent normal tissues using 16S rRNA gene sequencing. This allowed us to characterize the bacterial communities within the ACC and explore potential associations between the bacterial community structure, patient clinical characteristics, and tumor molecular features obtained through RNA sequencing. The bacterial composition in the ACC was significantly different from that in adjacent normal salivary tissue, and the ACC exhibited diverse levels of species richness. We identified two main microbial subtypes within the ACC: oral-like and gut-like. Oral-like microbiomes, characterized by increased diversity and abundance of Neisseria, Leptotrichia, Actinomyces, Streptococcus, Rothia, and Veillonella (commonly found in healthy oral cavities), were associated with a less aggressive ACC-II molecular subtype and improved patient outcomes. Notably, we identified the same oral genera in oral cancer and head and neck squamous cell carcinomas. In both cancers, they were part of shared oral communities associated with a more diverse microbiome, less aggressive tumor phenotype, and better survival that reveal the genera as potential pancancer biomarkers for favorable microbiomes in ACC and other head and neck cancers. Conversely, gut-like intratumoral microbiomes, which feature low diversity and colonization by gut mucus layer-degrading species, such as Bacteroides, Akkermansia, Blautia, Bifidobacterium, and Enterococcus, were associated with poorer outcomes. Elevated levels of Bacteroides thetaiotaomicron were independently associated with significantly worse survival and positively correlated with tumor cell biosynthesis of glycan-based cell membrane components.
Collapse
Affiliation(s)
- Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ivonne I Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren K McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasmine M Hoballah
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fabiana J Veguilla
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Renata Ferrarotto
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew P Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adel K El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
6
|
Schaus SR, Vasconcelos Pereira G, Luis AS, Madlambayan E, Terrapon N, Ostrowski MP, Jin C, Henrissat B, Hansson GC, Martens EC. Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron. mBio 2024:e0003924. [PMID: 38975756 DOI: 10.1128/mbio.00039-24] [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: 01/10/2024] [Accepted: 05/23/2024] [Indexed: 07/09/2024] Open
Abstract
Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques-a known mucin degrader that has been implicated in inflammatory bowel diseases (IBDs)-degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong α-L-fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which might contribute to its association with IBD.IMPORTANCEAn important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade the various components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate species associated with bacterial mucus damage and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another species of gut bacteria, Bacteroides thetaiotaomicron. Our findings underscore the importance of understanding mucin degradation mechanisms in different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately affect mucus damage and could therefore be key players in effects that result from reductions in mucus integrity.
Collapse
Affiliation(s)
- Sadie R Schaus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Ana S Luis
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Emily Madlambayan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille University, Marseille, France
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
7
|
Sreya PK, Hari Naga Papa Rao A, Suresh G, Sasikala C, Venkata Ramana C. Genomic and functional insights of a mucin foraging Rhodopirellula halodulae sp. nov. Syst Appl Microbiol 2024; 47:126523. [PMID: 38897058 DOI: 10.1016/j.syapm.2024.126523] [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: 02/10/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the Rhodopirellula genus. The type strain was identified as JC737T, which shared 99.1 % 16S rRNA gene sequence identity with Rhodopirellula baltica SH1T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and dDDH values of the strain JC737T were 75.8-76.1 % and 20.8-21.3 %, respectively, in comparison to other Rhodopirellula members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum Planctomycetota. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as Rhodopirellula halodulae sp. nov.
Collapse
Affiliation(s)
- P K Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Atham Hari Naga Papa Rao
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | | | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.
| |
Collapse
|
8
|
Panyod S, Wu WK, Chang CT, Wada N, Ho HC, Lo YL, Tsai SP, Chen RA, Huang HS, Liu PY, Chen YH, Chuang HL, Shen TCD, Tang SL, Ho CT, Wu MS, Sheen LY. Common dietary emulsifiers promote metabolic disorders and intestinal microbiota dysbiosis in mice. Commun Biol 2024; 7:749. [PMID: 38902371 PMCID: PMC11190199 DOI: 10.1038/s42003-024-06224-3] [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: 03/24/2023] [Accepted: 04/22/2024] [Indexed: 06/22/2024] Open
Abstract
Dietary emulsifiers are linked to various diseases. The recent discovery of the role of gut microbiota-host interactions on health and disease warrants the safety reassessment of dietary emulsifiers through the lens of gut microbiota. Lecithin, sucrose fatty acid esters, carboxymethylcellulose (CMC), and mono- and diglycerides (MDG) emulsifiers are common dietary emulsifiers with high exposure levels in the population. This study demonstrates that sucrose fatty acid esters and carboxymethylcellulose induce hyperglycemia and hyperinsulinemia in a mouse model. Lecithin, sucrose fatty acid esters, and CMC disrupt glucose homeostasis in the in vitro insulin-resistance model. MDG impairs circulating lipid and glucose metabolism. All emulsifiers change the intestinal microbiota diversity and induce gut microbiota dysbiosis. Lecithin, sucrose fatty acid esters, and CMC do not impact mucus-bacterial interactions, whereas MDG tends to cause bacterial encroachment into the inner mucus layer and enhance inflammation potential by raising circulating lipopolysaccharide. Our findings demonstrate the safety concerns associated with using dietary emulsifiers, suggesting that they could lead to metabolic syndromes.
Collapse
Affiliation(s)
- Suraphan Panyod
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
- Center for Food and Biomolecules, National Taiwan University, Taipei, Taiwan, ROC
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Wei-Kai Wu
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan, ROC
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
- Bachelor Program of Biotechnology and Food Nutrition, National Taiwan University, Taipei, Taiwan, ROC
| | - Chih-Ting Chang
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Han-Chen Ho
- Department of Anatomy, Tzu Chi University, Hualien, Taiwan, ROC
| | - Yi-Ling Lo
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Sing-Ping Tsai
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Rou-An Chen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
| | - Huai-Syuan Huang
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
| | - Po-Yu Liu
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan, ROC
| | - Yi-Hsun Chen
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Hsiao-Li Chuang
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei, Taiwan, ROC
| | - Ting-Chin David Shen
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ, USA
| | - Ming-Shiang Wu
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC.
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC.
| | - Lee-Yan Sheen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan, ROC.
- Center for Food and Biomolecules, National Taiwan University, Taipei, Taiwan, ROC.
- National Center for Food Safety Education and Research, National Taiwan University, Taipei, Taiwan, ROC.
| |
Collapse
|
9
|
Fricker AD, Yao T, Lindemann SR, Flores GE. Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage. FEMS Microbiol Ecol 2024; 100:fiae078. [PMID: 38794902 PMCID: PMC11180985 DOI: 10.1093/femsec/fiae078] [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: 10/03/2023] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024] Open
Abstract
Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.
Collapse
Affiliation(s)
- Ashwana D Fricker
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Gilberto E Flores
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
| |
Collapse
|
10
|
Li Y, Qi X, Wang Q, He Y, Li Z, Cen X, Wei L. Comprehensive analysis of key host gene-microbe networks in the cecum tissues of the obese rabbits induced by a high-fat diet. Front Cell Infect Microbiol 2024; 14:1407051. [PMID: 38947127 PMCID: PMC11211605 DOI: 10.3389/fcimb.2024.1407051] [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: 03/26/2024] [Accepted: 05/24/2024] [Indexed: 07/02/2024] Open
Abstract
The Cecum is a key site for cellulose digestion in nutrient metabolism of intestine, but its mechanisms of microbial and gene interactions has not been fully elucidated during pathogenesis of obesity. Therefore, the cecum tissues of the New Zealand rabbits and their contents between the high-fat diet-induced group (Ob) and control group (Co) were collected and analyzed using multi-omics. The metagenomic analysis indicated that the relative abundances of Corallococcus_sp._CAG:1435 and Flavobacteriales bacterium species were significantly lower, while those of Akkermansia glycaniphila, Clostridium_sp._CAG:793, Mycoplasma_sp._CAG:776, Mycoplasma_sp._CAG:472, Clostridium_sp._CAG:609, Akkermansia_sp._KLE1605, Clostridium_sp._CAG:508, and Firmicutes_bacterium_CAG:460 species were significantly higher in the Ob as compared to those in Co. Transcriptomic sequencing results showed that the differentially upregulated genes were mainly enriched in pathways, including calcium signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway, while the differentially downregulated genes were mainly enriched in pathways of NF-kappaB signaling pathway and T cell receptor signaling pathway. The comparative analysis of metabolites showed that the glycine, serine, and threonine metabolism and cysteine and methionine metabolism were the important metabolic pathways between the two groups. The combined analysis showed that CAMK1, IGFBP6, and IGFBP4 genes were highly correlated with Clostridium_sp._CAG:793, and Akkermansia_glycaniphila species. Thus, the preliminary study elucidated the microbial and gene interactions in cecum of obese rabbit and provided a basis for further studies in intestinal intervention for human obesity.
Collapse
Affiliation(s)
- Yanhong Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan He
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhupeng Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xi Cen
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Limin Wei
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| |
Collapse
|
11
|
Muramatsu MK, Winter SE. Nutrient acquisition strategies by gut microbes. Cell Host Microbe 2024; 32:863-874. [PMID: 38870902 PMCID: PMC11178278 DOI: 10.1016/j.chom.2024.05.011] [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: 03/25/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
The composition and function of the gut microbiota are intimately tied to nutrient acquisition strategies and metabolism, with significant implications for host health. Both dietary and host-intrinsic factors influence community structure and the basic modes of bacterial energy metabolism. The intestinal tract is rich in carbon and nitrogen sources; however, limited access to oxygen restricts energy-generating reactions to fermentation. By contrast, increased availability of electron acceptors during episodes of intestinal inflammation results in phylum-level changes in gut microbiota composition, suggesting that bacterial energy metabolism is a key driver of gut microbiota function. In this review article, we will illustrate diverse examples of microbial nutrient acquisition strategies in the context of habitat filters and anatomical location and the central role of energy metabolism in shaping metabolic strategies to support bacterial growth in the mammalian gut.
Collapse
Affiliation(s)
- Matthew K Muramatsu
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA
| | - Sebastian E Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA.
| |
Collapse
|
12
|
Yarahmadi A, Heidari S, Sepahvand P, Afkhami H, Kheradjoo H. Microplastics and environmental effects: investigating the effects of microplastics on aquatic habitats and their impact on human health. Front Public Health 2024; 12:1411389. [PMID: 38912266 PMCID: PMC11191580 DOI: 10.3389/fpubh.2024.1411389] [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: 04/02/2024] [Accepted: 05/13/2024] [Indexed: 06/25/2024] Open
Abstract
Microplastics (MPs) are particles with a diameter of <5 mm. The disposal of plastic waste into the environment poses a significant and pressing issue concern globally. Growing worry has been expressed in recent years over the impact of MPs on both human health and the entire natural ecosystem. MPs impact the feeding and digestive capabilities of marine organisms, as well as hinder the development of plant roots and leaves. Numerous studies have shown that the majority of individuals consume substantial quantities of MPs either through their dietary intake or by inhaling them. MPs have been identified in various human biological samples, such as lungs, stool, placenta, sputum, breast milk, liver, and blood. MPs can cause various illnesses in humans, depending on how they enter the body. Healthy and sustainable ecosystems depend on the proper functioning of microbiota, however, MPs disrupt the balance of microbiota. Also, due to their high surface area compared to their volume and chemical characteristics, MPs act as pollutant absorbers in different environments. Multiple policies and initiatives exist at both the domestic and global levels to mitigate pollution caused by MPs. Various techniques are currently employed to remove MPs, such as biodegradation, filtration systems, incineration, landfill disposal, and recycling, among others. In this review, we will discuss the sources and types of MPs, the presence of MPs in different environments and food, the impact of MPs on human health and microbiota, mechanisms of pollutant adsorption on MPs, and the methods of removing MPs with algae and microbes.
Collapse
Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | | | - Parisa Sepahvand
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
| | | |
Collapse
|
13
|
Cheng J, Kolba N, Tako E. The effect of dietary zinc and zinc physiological status on the composition of the gut microbiome in vivo. Crit Rev Food Sci Nutr 2024; 64:6432-6451. [PMID: 36688291 DOI: 10.1080/10408398.2023.2169857] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Zinc serves critical catalytic, regulatory, and structural roles. Hosts and their resident gut microbiota both require zinc, leading to competition, where a balance must be maintained. This systematic review examined evidence on dietary zinc and physiological status (zinc deficiency or high zinc/zinc overload) effects on gut microbiota. This review was conducted according to PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines and registered in PROSPERO (CRD42021250566). PubMed, Web of Science, and Scopus databases were searched for in vivo (animal) studies, resulting in eight selected studies. Study quality limitations were evaluated using the SYRCLE risk of bias tool and according to ARRIVE guidelines. The results demonstrated that zinc deficiency led to inconsistent changes in α-diversity and short-chain fatty acid production but led to alterations in bacterial taxa with functions in carbohydrate metabolism, glycan metabolism, and intestinal mucin degradation. High dietary zinc/zinc overload generally resulted in either unchanged or decreased α-diversity, decreased short-chain fatty acid production, and increased bacterial metal resistance and antibiotic resistance genes. Additional studies in human and animal models are needed to further understand zinc physiological status effects on the intestinal microbiome and clarify the applicability of utilizing the gut microbiome as a potential zinc status biomarker.
Collapse
Affiliation(s)
- Jacquelyn Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Nikolai Kolba
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Elad Tako
- Department of Food Science, Cornell University, Ithaca, New York, USA
| |
Collapse
|
14
|
Rocha ST, Shah DD, Shrivastava A. Ecological, beneficial, and pathogenic functions of the Type 9 Secretion System. Microb Biotechnol 2024; 17:e14516. [PMID: 38924452 PMCID: PMC11205867 DOI: 10.1111/1751-7915.14516] [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: 03/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The recently discovered Type 9 Secretion System (T9SS) is present in bacteria of the Fibrobacteres-Bacteroidetes-Chlorobi superphylum, which are key constituents of diverse microbiomes. T9SS is instrumental in the extracellular secretion of over 270,000 proteins, including peptidases, sugar hydrolases, metal ion-binding proteins, and metalloenzymes. These proteins are essential for the interaction of bacteria with their environment. This mini-review explores the extensive array of proteins secreted by the T9SS. It highlights the diverse functions of these proteins, emphasizing their roles in pathogenesis, bacterial interactions, host colonization, and the overall health of the ecosystems inhabited by T9SS-containing bacteria.
Collapse
Affiliation(s)
- Sofia T. Rocha
- Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Dhara D. Shah
- Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Mathematical and Natural SciencesArizona State UniversityGlendaleArizonaUSA
| | - Abhishek Shrivastava
- Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| |
Collapse
|
15
|
Li W, Lin X, Liang H, Wu Z, Wang M, Sun J, Li X, He W, Gao X, Hu T, Xiao L, Zou Y. Genomic and functional diversity of the human-derived isolates of Faecalibacterium. Front Microbiol 2024; 15:1379500. [PMID: 38873165 PMCID: PMC11169845 DOI: 10.3389/fmicb.2024.1379500] [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: 01/31/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Faecalibacterium is one of the most abundant bacteria in the gut microbiota of healthy adults, highly regarded as a next-generation probiotic. However, the functions of Faecalibacterium genomes from cultured strains and the distribution of different species in populations may differ among different sources. Methods We here performed an extensive analysis of pan-genomes, functions, and safety evaluation of 136 Faecalibacterium genomes collected from 10 countries. Results The genomes are clustered into 11 clusters, with only five of them were characterized and validly nomenclated. Over 80% of the accessory genes and unique genes of Faecalibacterium are found with unknown function, which reflects the importance of expanding the collection of Faecalibacterium strains. All the genomes have the potential to produce acetic acid and butyric acid. Nine clusters of Faecalibacterium are found significantly enriched in the healthy individuals compared with patients with type II diabetes.. Discussion This study provides a comprehensive view of genomic characteristic and functions and of culturable Faecalibacterium bacterium from human gut, and enables clinical advances in the future.
Collapse
Affiliation(s)
- Wenxi Li
- BGI-Shenzhen, Shenzhen, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hewei Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Wang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingxi Sun
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofang Li
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | | | - Tongyuan Hu
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark
| |
Collapse
|
16
|
Suda Y, Nakamura K, Matsuyama F, Hamada Y, Makabe H, Narita M, Nagumo Y, Mori T, Kuzumaki N, Narita M. Peripheral-central network analysis of cancer cachexia status accompanied by the polarization of hypothalamic microglia with low expression of inhibitory immune checkpoint receptors. Mol Brain 2024; 17:20. [PMID: 38685046 PMCID: PMC11059753 DOI: 10.1186/s13041-024-01091-9] [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: 11/30/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
While the excessive inflammation in cancer cachexia is well-known to be induced by the overproduction of inflammatory mediators in the periphery, microflora disruption and brain dysfunction are also considered to contribute to the induction of cancer cachexia. Hypothalamic microglia play a crucial role in brain inflammation and central-peripheral immune circuits via the production of inflammatory mediators. In the present study, we evaluated possible changes in excessive secretion of gut microbiota-derived endotoxin and the expression timeline of several inflammation-regulatory mediators and their inhibiting modulators in hypothalamic microglia of a mouse model of cancer cachexia following transplantation of pancreatic cancer cells. We demonstrated that the plasma level of lipopolysaccharide (LPS) was significantly increased with an increase in anaerobic bacteria, especially Firmicutes, in the gut at the late stage of tumor-bearing mice that exhibited dramatic appetite loss, sarcopenia and severe peripheral immune suppression. At the early stage, in which tumor-bearing mice had not yet displayed "cachexia symptoms", the mRNA expression of pro-inflammatory cytokines, but not of the neurodegenerative and severe inflammatory modulator lipocalin-2 (LCN2), was significantly increased, whereas at the late "cachexia stage", the level of LCN2 mRNA was significantly increased along with significant decreases in levels of inhibitory immune checkpoint receptors programmed death receptor-1 (PD-1) and CD112R in hypothalamic microglia. In addition, a high density of activated neurons in the paraventricular nucleus (PVN) of the hypothalamus region and a significant increase in corticosterone secretion were found in cachexia model mice. Related to the cachexia state, released corticosterone was clearly increased in normal mice with specific activation of PVN neurons. A marked decrease in the natural killer cell population was also observed in the spleen of mice with robust activation of PVN neurons as well as mice with cancer cachexia. On the other hand, in vivo administration of LPS in normal mice induced hypothalamic microglia with low expression of inhibitory immune checkpoint receptors. These findings suggest that the induction of cancer cachexia may parallel exacerbation of the hypothalamic inflammatory status with polarization to microglia expressed with low levels of inhibitory immune checkpoint receptors following LPS release from the gut microflora.
Collapse
Affiliation(s)
- Yukari Suda
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Keiko Nakamura
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
- Department of Pharmacy, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Fukiko Matsuyama
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
- Japan Small Animal Medical Center, 1-10-4 Higashitokorozawawada, Tokorozawa-Shi, Saitama, 359-0023, Japan
| | - Yusuke Hamada
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hitoshi Makabe
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Michiko Narita
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yasuyuki Nagumo
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Tomohisa Mori
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan
| | - Naoko Kuzumaki
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan.
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
| | - Minoru Narita
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-Ku, Tokyo, 142-8501, Japan.
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
| |
Collapse
|
17
|
Holmberg SM, Feeney RH, Prasoodanan P K V, Puértolas-Balint F, Singh DK, Wongkuna S, Zandbergen L, Hauner H, Brandl B, Nieminen AI, Skurk T, Schroeder BO. The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids. Nat Commun 2024; 15:3502. [PMID: 38664378 PMCID: PMC11045866 DOI: 10.1038/s41467-024-47594-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: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the gut bacterial configuration and disturbs this microbe-mucus interaction, but the specific bacteria and microbial metabolites responsible for maintaining mucus function remain poorly understood. By using human-to-mouse microbiota transplantation and ex vivo analysis of colonic mucus function, we here show as a proof-of-concept that individuals who increase their daily dietary fiber intake can improve the capacity of their gut microbiota to prevent diet-mediated mucus defects. Mucus growth, a critical feature of intact colonic mucus, correlated with the abundance of the gut commensal Blautia, and supplementation of Blautia coccoides to mice confirmed its mucus-stimulating capacity. Mechanistically, B. coccoides stimulated mucus growth through the production of the short-chain fatty acids propionate and acetate via activation of the short-chain fatty acid receptor Ffar2, which could serve as a new target to restore mucus growth during mucus-associated lifestyle diseases.
Collapse
Affiliation(s)
- Sandra M Holmberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Rachel H Feeney
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Vishnu Prasoodanan P K
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Fabiola Puértolas-Balint
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Dhirendra K Singh
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Supapit Wongkuna
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Lotte Zandbergen
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Hans Hauner
- Institute in Nutritional Medicine, TU Munich, Munich, Germany
- TU Munich, School of Medicine, Munich, Germany
| | - Beate Brandl
- ZIEL Institute for Food and Health, TU Munich, Munich, Germany
| | - Anni I Nieminen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Thomas Skurk
- ZIEL Institute for Food and Health, TU Munich, Munich, Germany
| | - Bjoern O Schroeder
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| |
Collapse
|
18
|
Culver RN, Spencer SP, Violette A, Lemus Silva EG, Takeuchi T, Nafarzadegan C, Higginbottom SK, Shalon D, Sonnenburg J, Huang KC. Improved mouse models of the small intestine microbiota using region-specific sampling from humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590999. [PMID: 38712253 PMCID: PMC11071525 DOI: 10.1101/2024.04.24.590999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function. In vitro culturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.
Collapse
Affiliation(s)
- Rebecca N. Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean Paul Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Arvie Violette
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Evelyn Giselle Lemus Silva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tadashi Takeuchi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ceena Nafarzadegan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dari Shalon
- Envivo Bio, Inc., San Francisco, CA 94107, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| |
Collapse
|
19
|
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
|
20
|
Kalenborn S, Zühlke D, Riedel K, Amann RI, Harder J. Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72. FEMS Microbiol Ecol 2024; 100:fiae045. [PMID: 38569650 PMCID: PMC11036162 DOI: 10.1093/femsec/fiae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Arabinose and galactose are major, rapidly metabolized components of marine particulate and dissolved organic matter. In this study, we observed for the first time large microbiomes for the degradation of arabinogalactan and report a detailed investigation of arabinogalactan utilization by the flavobacterium Maribacter sp. MAR_2009_72. Cellular extracts hydrolysed arabinogalactan in vitro. Comparative proteomic analyses of cells grown on arabinogalactan, arabinose, galactose, and glucose revealed the expression of specific proteins in the presence of arabinogalactan, mainly glycoside hydrolases (GH). Extracellular glycan hydrolysis involved five alpha-l-arabinofuranosidases affiliating with glycoside hydrolase families 43 and 51, four unsaturated rhamnogalacturonylhydrolases (GH105) and a protein with a glycoside hydrolase family-like domain. We detected expression of three induced TonB-dependent SusC/D transporter systems, one SusC, and nine glycoside hydrolases with a predicted periplasmatic location. These are affiliated with the families GH3, GH10, GH29, GH31, GH67, GH78, and GH115. The genes are located outside of and within canonical polysaccharide utilization loci classified as specific for arabinogalactan, for galactose-containing glycans, and for arabinose-containing glycans. The breadth of enzymatic functions expressed in Maribacter sp. MAR_2009_72 as response to arabinogalactan from the terrestrial plant larch suggests that Flavobacteriia are main catalysts of the rapid turnover of arabinogalactans in the marine environment.
Collapse
Affiliation(s)
- Saskia Kalenborn
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| |
Collapse
|
21
|
Gonza I, Goya-Jorge E, Douny C, Boutaleb S, Taminiau B, Daube G, Scippo ML, Louis E, Delcenserie V. Food additives impair gut microbiota from healthy individuals and IBD patients in a colonic in vitro fermentation model. Food Res Int 2024; 182:114157. [PMID: 38519184 DOI: 10.1016/j.foodres.2024.114157] [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: 11/06/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
Intestinal fibrosis is a long-term complication of inflammatory bowel diseases (IBD). Changes in microbial populations have been linked with the onset of fibrosis and some food additives are known to promote intestinal inflammation facilitating fibrosis induction. In this study, we investigated how polysorbate 80, sucralose, titanium dioxide, sodium nitrite and maltodextrin affect the gut microbiota and the metabolic activity in healthy and IBD donors (patients in remission and with a flare of IBD). The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) with a static (batch) configuration was used to evaluate the effects of food additives on the human intestinal microbiota. Polysorbate 80 and sucralose decreased butyrate-producing bacteria such as Roseburia and Faecalibacterium prausnitzii. Both compounds, also increased bacterial species positively correlated with intestinal inflammation and fibrosis (i.e.: Enterococcus, Veillonella and Mucispirillum schaedleri), especially in donors in remission of IBD. Additionally, polysorbate 80 induced a lower activity of the aryl hydrocarbon receptor (AhR) in the three groups of donors, which can affect the intestinal homeostasis. Maltodextrin, despite increasing short-chain fatty acids production, promoted the growth of Ruminococcus genus, correlated with higher risk of fibrosis, and decreased Oscillospira which is negatively associated with fibrosis. Our findings unveil crucial insights into the potential deleterious effects of polysorbate 80, sucralose and maltodextrin on human gut microbiota in healthy and, to a greater extent, in IBD patients.
Collapse
Affiliation(s)
- Irma Gonza
- Laboratory of Food Quality Management, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Elizabeth Goya-Jorge
- Laboratory of Food Quality Management, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Caroline Douny
- Laboratory of Food Analysis, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Samiha Boutaleb
- Laboratory of Food Analysis, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Bernard Taminiau
- Laboratory of Microbiology, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Georges Daube
- Laboratory of Microbiology, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Marie-Louise Scippo
- Laboratory of Food Analysis, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| | - Edouard Louis
- Hepato - Gastroenterology and Digestive Oncology Department, CHU of Liège, Liège, Belgium.
| | - Véronique Delcenserie
- Laboratory of Food Quality Management, Department of Food Sciences, FARAH - Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium.
| |
Collapse
|
22
|
Li S, Chen M, Wang Z, Abudourexiti W, Zhang L, Ding C, Ding L, Gong J. Ant may well destroy a whole dam: glycans of colonic mucus barrier disintegrated by gut bacteria. Microbiol Res 2024; 281:127599. [PMID: 38219635 DOI: 10.1016/j.micres.2023.127599] [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: 09/25/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The colonic mucus layer plays a critical role in maintaining the integrity of the colonic mucosal barrier, serving as the primary defense against colonic microorganisms. Predominantly composed of mucin 2 (MUC2), a glycosylation-rich protein, the mucus layer forms a gel-like coating that covers the colonic epithelium surface. This layer provides a habitat for intestinal microorganisms, which can utilize mucin glycans present in the mucus layer as a sustainable source of nutrients. Additionally, metabolites produced by the microbiota during the metabolism of mucus glycans have a profound impact on host health. Under normal conditions, the production and consumption of mucus maintain a dynamic balance. However, several studies have demonstrated that certain factors, such as dietary fiber deficiency, can enhance the metabolism of mucus glycans by gut bacteria, thereby disturbing this balance and weakening the mucus barrier function of the mucus layer. To better understand the occurrence and development of colon-related diseases, it is crucial to investigate the complex metabolic patterns of mucus glycosylation by intestinal microorganisms. Our objective was to comprehensively review these patterns in order to clarify the effects of mucus layer glycan metabolism by intestinal microorganisms on the host.
Collapse
Affiliation(s)
- Song Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Mingfei Chen
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zhongyuan Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Waresi Abudourexiti
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Liang Zhang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Jiangsu, China
| | - Chao Ding
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China.
| |
Collapse
|
23
|
Reis SK, Socca EAR, de Souza BR, Genaro SC, Durán N, Fávaro WJ. Effects of probiotic supplementation on chronic inflammatory process modulation in colorectal carcinogenesis. Tissue Cell 2024; 87:102293. [PMID: 38244400 DOI: 10.1016/j.tice.2023.102293] [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: 09/17/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/22/2024]
Abstract
The current study investigated the potential effects of probiotic supplementation on colorectal carcinogenesis chemically induced with 1,2-dimethylhydrazine (DMH) and treated with 5-fluorouracil (5FU)-based chemotherapy in mice. Animals were randomly allocated in five different groups: Control: which not receive any treatment throughout the experimental course; Colitis model group (DMH): treated with DMH; DMH+ 5FU: animals received I.P. (intraperitoneal) dose of chemotherapy on a weekly basis; DMH+PROB: animals received daily administrations (via gavage) of probiotics (Lactobacillus: acidophilus and paracasei, Bifidobacterium lactis and bifidum); and DMH+ PROB+ 5FU: animals received the same treatment as the previous groups. After ten-week treatment, mice's large intestine was collected and subjected to colon length, histopathological, periodic acid-schiff (PAS) staining and immunohistochemistry (TLR2, MyD88, NF-κB, IL-6, TLR4, TRIF, IRF-3, IFN-γ, Ki-67, KRAS, p53, IL-10, and TGF-β) analyzes. Variance (ANOVA) and Kruskal-Wallis tests were used for statistical analysis, at significance level p 0.05. Probiotics' supplementation has increased the production of Ki-67 cell-proliferation marker, reduced body weight, and colon shortening, as well as modulated the chronic inflammatory process in colorectal carcinogenesis by inhibiting NF-κB expression and mitigating mucin depletion. Thus, these findings lay a basis for guide future studies focused on probiotics' action mechanisms in tumor microenvironment which might have implications in clinical practice.
Collapse
Affiliation(s)
- Sabrina Karen Reis
- Faculty Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil; Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil.
| | - Eduardo Augusto Rabelo Socca
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bianca Ribeiro de Souza
- British Columbia's Gynecological Cancer Research (OVCARE) Program and Department of Obstetrics and Gynecology, University of British Columbia, Vancouver General Hospital, Vancouver, BC, Canada.
| | | | - Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil; Nanomedicine Research Unit (Nanomed), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - Wagner José Fávaro
- Faculty Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil; Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| |
Collapse
|
24
|
Wang Z, Shen J. The role of goblet cells in Crohn' s disease. Cell Biosci 2024; 14:43. [PMID: 38561835 PMCID: PMC10985922 DOI: 10.1186/s13578-024-01220-w] [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: 06/01/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
The prevalence of Crohn's disease (CD), a subtype of inflammatory bowel disease (IBD), is increasing worldwide. The pathogenesis of CD is hypothesized to be related to environmental, genetic, immunological, and bacterial factors. Current studies have indicated that intestinal epithelial cells, including columnar, Paneth, M, tuft, and goblet cells dysfunctions, are strongly associated with these pathogenic factors. In particular, goblet cells dysfunctions have been shown to be related to CD pathogenesis by direct or indirect ways, according to the emerging studies. The mucus barrier was established with the help of mucins secreted by goblet cells. Not only do the mucins mediate the mucus barrier permeability and bacterium selection, but also, they are closely linked with the endothelial reticulum stress during the synthesis process. Goblet cells also play a vital role in immune response. It was indicated that goblet cells take part in the antigen presentation and cytokines secretion process. Disrupted goblet cells related immune process were widely discovered in CD patients. Meanwhile, dysbiosis of commensal and pathogenic microbiota can induce myriad immune responses through mucus and goblet cell-associated antigen passage. Microbiome dysbiosis lead to inflammatory reaction against pathogenic bacteria and abnormal tolerogenic response. All these three pathways, including the loss of mucus barrier function, abnormal immune reaction, and microbiome dysbiosis, may have independent or cooperative effect on the CD pathogenesis. However, many of the specific mechanisms underlying these pathways remain unclear. Based on the current understandings of goblet cell's role in CD pathogenesis, substances including butyrate, PPARγagonist, Farnesoid X receptor agonist, nuclear factor-Kappa B, nitrate, cytokines mediators, dietary and nutrient therapies were all found to have potential therapeutic effects on CD by regulating the goblet cells mediated pathways. Several monoclonal antibodies already in use for the treatment of CD in the clinical settings were also found to have some goblet cells related therapeutic targets. In this review, we introduce the disease-related functions of goblet cells, their relationship with CD, their possible mechanisms, and current CD treatments targeting goblet cells.
Collapse
Affiliation(s)
- Zichen Wang
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Ministry of Health, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, No.160 PuJian Road, Shanghai, 200127, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Ministry of Health, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, No.160 PuJian Road, Shanghai, 200127, China.
| |
Collapse
|
25
|
Pang H, Zheng K, Wang W, Zheng M, Liu Y, Yin H, Zhang D. Cefotaxime Exposure-Caused Oxidative Stress, Intestinal Damage and Gut Microbial Disruption in Artemia sinica. Microorganisms 2024; 12:675. [PMID: 38674619 PMCID: PMC11052325 DOI: 10.3390/microorganisms12040675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Cefotaxime (CTX) is an easily detectable antibiotic pollutant in the water environment, but little is known about its toxic effects on aquatic invertebrates, especially on the intestine. Here, we determined the oxidative stress conditions of A. sinica under CTX exposure with five concentrations (0, 0.001, 0.01, 0.1 and 1 mg/L) for 14 days. After that, we focused on changes in intestinal tissue morphology and gut microbiota in A. sinica caused by CTX exposure at 0.01 mg/L. We found malondialdehyde (MDA) was elevated in CTX treatment groups, suggesting the obvious antibiotic-induced oxidative stress. We also found CTX exposure at 0.01 mg/L decreased the villus height and muscularis thickness in gut tissue. The 16S rRNA gene analysis indicated that CTX exposure reshaped the gut microbiota diversity and community composition. Proteobacteria, Actinobacteriota and Bacteroidota were the most widely represented phyla in A. sinica gut. The exposure to CTX led to the absence of Verrucomicrobia in dominant phyla and an increase in Bacteroidota abundance. At the genus level, eleven genera with an abundance greater than 0.1% exhibited statistically significant differences among groups. Furthermore, changes in gut microbiota composition were accompanied by modifications in gut microbiota functions, with an up-regulation in amino acid and drug metabolism functions and a down-regulation in xenobiotic biodegradation and lipid metabolism-related functions under CTX exposure. Overall, our study enhances our understanding of the intestinal damage and microbiota disorder caused by the cefotaxime pollutant in aquatic invertebrates, which would provide guidance for healthy aquaculture.
Collapse
Affiliation(s)
- Huizhong Pang
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
| | - Kaixuan Zheng
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
| | - Wenbo Wang
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
| | - Mingjuan Zheng
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
| | - Yudan Liu
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
| | - Hong Yin
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Daochuan Zhang
- The International Centre for Precision Environmental Health and Governance, College of Life Sciences, Hebei University, Baoding 071002, China; (H.P.); (K.Z.); (W.W.); (M.Z.)
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| |
Collapse
|
26
|
Kulkarni BS, Makde RD, Jamdar SN. Characterization of a secreted aminopeptidase of M28 family from B. fragilis and its possible role in protein metabolism in the gut. Biochim Biophys Acta Gen Subj 2024; 1868:130598. [PMID: 38499114 DOI: 10.1016/j.bbagen.2024.130598] [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: 11/09/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Products of microbial protein metabolism in the gut can influence the health of the host in many ways. Members of the Bacteriodales, major commensals of the human colon have been associated with long-term intake of high-protein diets. Undigested proteins or peptides that reach the colon can be hydrolyzed by extra-cellular proteases found in some Bacteroides species into amino acids and peptides which can be further catabolized. In this communication, we have characterized one such secreted aminopeptidase (BfAP) from Bacteroides fragilis belonging to the M28 family which is capable of degrading peptides released from soybean protein after predigestion in the small intestine. The BfAP enzyme was cloned, expressed in E. coli, and purified to homogeneity. It is a metallopeptidase requiring Co2+ ion for optimum activity at 55 °C and pH 8 and preferentially cleaves neutral aliphatic (Met/Leu) and positively charged (Arg/Lys) amino acids from the N-terminus of peptides. It showed high specificity for long peptides as well as proteins like β-casein. Structural analysis of BfAP and its orthologues using AlphaFold2 reveal a shared highly conserved M28 domain, but vary with respect to their N-terminal region with some of them possessing an additional cap domain which may be important for regulation of substrate binding. Although BfAP lacks the typical cap domain, it shows small extensions that can form a loop adjacent to the proposed active site and may affect substrate binding. We suggest that this secreted enzyme may play an important role in protein metabolism in the colon where Bacteroides species are abundant.
Collapse
Affiliation(s)
- Bhushan S Kulkarni
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences Department, Homi Bhabha National Institute, Mumbai 400094, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences Department, Homi Bhabha National Institute, Mumbai 400094, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences Department, Homi Bhabha National Institute, Mumbai 400094, India.
| |
Collapse
|
27
|
Lackner S, Mahnert A, Moissl-Eichinger C, Madl T, Habisch H, Meier-Allard N, Kumpitsch C, Lahousen T, Kohlhammer-Dohr A, Mörkl S, Strobl H, Holasek S. Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes-secondary analysis of a randomized placebo-controlled parallel intervention trial. MICROBIOME 2024; 12:49. [PMID: 38461313 PMCID: PMC10924357 DOI: 10.1186/s40168-024-01774-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints. Given the importance of the gut microbiome in food digestion, we investigated in this secondary analysis of the randomized placebo-controlled parallel intervention study (ClinicalTrials.gov registration: NCT05432362) if aronia juice tolerability was associated with changes in intestinal microbiota and bacterial metabolites, seeking for potential mechanistic insights into the impact on aronia polyphenol tolerance and metabolic outcomes. RESULTS Forty females were enrolled for this 6-week trial, receiving either 100 ml natural aronia juice (verum, V) twice daily or a polyphenol-free placebo (P) with a similar nutritional profile, followed by a 6-week washout. Within V, individuals were categorized into those who tolerated the juice well (Vt) or reported complaints (Vc). The gut microbiome diversity, as analyzed by 16S rRNA gene-based next-generation sequencing, remained unaltered in Vc but changed significantly in Vt. A MICOM-based flux balance analysis revealed pronounced differences in the 40 most predictive metabolites post-intervention. In Vc carbon-dioxide, ammonium and nine O-glycans were predicted due to a shift in microbial composition, while in Vt six bile acids were the most likely microbiota-derived metabolites. NMR metabolomics of plasma confirmed increased lipoprotein subclasses (LDL, VLDL) post-intervention, reverting after wash out. Stool samples maintained a stable metabolic profile. CONCLUSION In linking aronia polyphenol tolerance to gut microbiota-derived metabolites, our study explores adaptive processes affecting lipoprotein profiles during high polyphenol ingestion in Vt and examines effects on mucosal gut health in response to intolerance to high polyphenol intake in Vc. Our results underpin the importance of individualized hormetic dosing for beneficial polyphenol effects, demonstrate dynamic gut microbiome responses to aronia juice, and emphasize personalized responses in polyphenol interventions.
Collapse
Affiliation(s)
- Sonja Lackner
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Tobias Madl
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Hansjörg Habisch
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Nathalie Meier-Allard
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Theresa Lahousen
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Alexandra Kohlhammer-Dohr
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Sabrina Mörkl
- Division of Medical Psychology, Psychosomatics and Psychotherapeutic Medicine, Auenbruggerplatz 3, 8036, Graz, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Sandra Holasek
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria.
| |
Collapse
|
28
|
Stepanova M, Aherne CM. Adenosine in Intestinal Epithelial Barrier Function. Cells 2024; 13:381. [PMID: 38474346 DOI: 10.3390/cells13050381] [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: 12/23/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
At the intestinal front, several lines of defense are in place to resist infection and injury, the mucus layer, gut microbiome and strong epithelial junctions, to name a few. Their collaboration creates a resilient barrier. In intestinal disorders, such as inflammatory bowel disease (IBD), barrier function is compromised, which results in rampant inflammation and tissue injury. In response to the destruction, the intestinal epithelium releases adenosine, a small but powerful nucleoside that functions as an alarm signal. Amidst the chaos of inflammation, adenosine aims to restore order. Within the scope of its effects is the ability to regulate intestinal epithelial barrier integrity. This review aims to define the contributions of adenosine to mucus production, microbiome-dependent barrier protection, tight junction dynamics, chloride secretion and acid-base balance to reinforce its importance in the intestinal epithelial barrier.
Collapse
Affiliation(s)
- Mariya Stepanova
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Carol M Aherne
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
29
|
Liu N, Kivenson V, Peng X, Cui Z, Lankiewicz TS, Gosselin KM, English CJ, Blair EM, O'Malley MA, Valentine DL. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Appl Environ Microbiol 2024; 90:e0091423. [PMID: 38265213 PMCID: PMC10880615 DOI: 10.1128/aem.00914-23] [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: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.
Collapse
Affiliation(s)
- Na Liu
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, China
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kelsey M. Gosselin
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chance J. English
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Ecology Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - Elaina M. Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Biological Engineering Program, University of California, Santa Barbara, California, USA
| | - David L. Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, California, USA
| |
Collapse
|
30
|
Meng P, Zhang G, Ma X, Ding X, Song X, Dang S, Yang R, Xu L. Traditional Chinese medicine (Xielikang) reduces diarrhea symptoms in acquired immune deficiency syndrome (AIDS) patients by regulating the intestinal microbiota. Front Microbiol 2024; 15:1346955. [PMID: 38435694 PMCID: PMC10904582 DOI: 10.3389/fmicb.2024.1346955] [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: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
Diarrheal acquired immune deficiency syndrome (AIDS) seriously affects the quality of life of patients. In this study, we analyzed the differences in the intestinal microbiota among healthy individuals, AIDS patients without diarrhea and AIDS patients with diarrhea through high-throughput sequencing. The microbial diversity in the intestines of patients in the AIDS diarrhea group was significantly increased, and after treatment with Xielikang, the intestinal microbial diversity returned to the baseline level. At the phylum level, compared those in to the healthy (ZC) and AIDS non diarrhea (FN) groups, the relative abundances of Bacteroidetes and Verrucomirobia in the AIDS diarrhea (FA) group before treatment were significantly increased, while the relative abundance of Firmicutes was significantly decreased. Similarly, compared with those in the FA group, the relative abundances of Bacteroidea and Firmicutes in the AIDS diarrhea (FB) group after treatment were significantly increased, while the relative abundance of Firmicutes was significantly decreased after treatment. Additionally, there was no significant difference between the ZC and FN groups. At the genus level, compared with those in the ZC group, the relative abundance of Prevotella and Escherichia_Shigella in the FA group was significantly increased, while the relative abundances of Megamonas and Bifidobacterium was significantly decreased compared to that in the ZC group. After treatment with Xielikang, the relative abundance of Prevotella and Escherichia_Shigella in the FB group were significantly decreased, while the relative abundances of Megamonas and Bifidobacteria were significantly increased than those in the FA group; moreover, there was no significant difference between the ZC and FN groups. The functional prediction results showed that the ketodeoxyoctonate (Kdo) transfer to lipid IVA III and the superpathway of N-acetylglucosamine pathways in the AIDS diarrhea group were significantly altered. The correlation analysis results showed that Dorea was positively correlated with inflammatory factors, while Streptococcus and Lactobacillus were negatively correlated with inflammatory factors. The composition and function of the intestinal microbiota changed significantly in AIDS diarrhea patients, which affected the immune function of the host. The Xielikang capsule modulated the composition of the intestinal microbiota in AIDS diarrhea patients and thus improved immune function and reduced diarrheal symptoms.
Collapse
Affiliation(s)
- Pengfei Meng
- Henan University of Chinese Medicine, Zhengzhou, China
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Guichun Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiuxia Ma
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xue Ding
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiyuan Song
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuyuan Dang
- Henan University of Chinese Medicine, Zhengzhou, China
| | - Ruihan Yang
- Henan University of Chinese Medicine, Zhengzhou, China
| | - Liran Xu
- Henan University of Chinese Medicine, Zhengzhou, China
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| |
Collapse
|
31
|
Blondeaux A, Valibouze C, Speca S, Rousseaux C, Dubuquoy C, Blanquart H, Zerbib P, Desreumaux P, Foligné B, Titécat M. Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management. Int J Mol Sci 2024; 25:2164. [PMID: 38396840 PMCID: PMC10889215 DOI: 10.3390/ijms25042164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.
Collapse
Affiliation(s)
- Aurélie Blondeaux
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Caroline Valibouze
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Silvia Speca
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
| | - Christel Rousseaux
- Intestinal Biotech Development, 1 Avenue Oscar Lambret, 59045 Lille, France; (C.R.); (C.D.)
| | - Caroline Dubuquoy
- Intestinal Biotech Development, 1 Avenue Oscar Lambret, 59045 Lille, France; (C.R.); (C.D.)
| | | | - Philippe Zerbib
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Pierre Desreumaux
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Benoît Foligné
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
| | - Marie Titécat
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
| |
Collapse
|
32
|
Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
Collapse
Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
| |
Collapse
|
33
|
Jank L, Bhargava P. Relationship Between Multiple Sclerosis, Gut Dysbiosis, and Inflammation: Considerations for Treatment. Neurol Clin 2024; 42:55-76. [PMID: 37980123 DOI: 10.1016/j.ncl.2023.07.005] [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: 11/20/2023]
Abstract
Multiple sclerosis is associated with gut dysbiosis, marked by changes in the relative abundances of specific microbes, circulating gut-derived metabolites, and altered gut permeability. This gut dysbiosis promotes disease pathology by increasing circulating proinflammatory bacterial factors, reducing tolerogenic factors, inducing molecular mimicry, and changing microbial nutrient metabolism. Beneficial antiinflammatory effects of the microbiome can be harnessed in therapeutic interventions. In the future, it is essential to assess the efficacy of these therapies in randomized controlled clinical trials to help make dietary and gut dysbiosis management an integral part of multiple sclerosis care.
Collapse
Affiliation(s)
- Larissa Jank
- Division of Neuroimmunology and Neurological Infections, Department of Neurology, Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Meyer 6-144, Baltimore, MD 21287, USA
| | - Pavan Bhargava
- Division of Neuroimmunology and Neurological Infections, Department of Neurology, Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Meyer 6-144, Baltimore, MD 21287, USA.
| |
Collapse
|
34
|
Miao Z, Chen L, Zhang Y, Zhang J, Zhang H. Bifidobacterium animalis subsp. lactis Probio-M8 alleviates abnormal behavior and regulates gut microbiota in a mouse model suffering from autism. mSystems 2024; 9:e0101323. [PMID: 38108654 PMCID: PMC10804959 DOI: 10.1128/msystems.01013-23] [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: 09/20/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
Probiotics can effectively improve a variety of neurological diseases, but there is little research on autism, and the specific mechanism is unclear. In this study, shotgun metagenomics analysis was used to investigate the preventive and therapeutic effects of Bifidobacterium animalis subsp. lactis Probio-M8 on autism. The results showed that Probio-M8 treatment significantly alleviated valproate (VPA)-induced autism in mice, with autistic symptoms characterized by increased stereotyped behaviors such as grooming, reduced learning ability, and decreased desire to socialize. Further studies have found that Probio-M8 can alleviate autism by optimizing gut microbiota diversity and regulating metabolic levels. Probio-M8 regulates gut microbiota structure by increasing the abundance of beneficial bacteria such as Bifidobacterium globosum and Akkermansia muciniphila. In addition, Probio-M8 regulates metabolic activity by increasing levels of choline, which corrects CAZy disorders. In conclusion, Probio-M8 is therapeutic in the VPA-induced autism mouse model by regulating the gut microbiome and metabolic levels.IMPORTANCEIndividuals with autism often exhibit symptoms of social invariance, obsessive-compulsive tendencies, and repetitive behaviors. However, early intervention and treatment can be effective in improving social skills and mitigating autism symptoms, including behaviors related to irritability. Although taking medication for autism may lead to side effects such as weight gain, probiotics can be an ideal intervention for alleviating these symptoms. In this study, we investigated the effects of Probio-M8 intervention on the behavior of autistic mice using an open-field test, a three-chamber sociability test, and a novel object recognition test. Metagenomic analysis revealed differences in gut microbiota diversity among groups, predicted changes in metabolite levels, and functionally annotated CAZy. Additionally, we analyzed serum neurotransmitter levels and found that probiotics were beneficial in mitigating neurotransmitter imbalances in mice with autism.
Collapse
Affiliation(s)
- Zhuangzhuang Miao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lin Chen
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Yong Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| |
Collapse
|
35
|
Goya-Jorge E, Gonza I, Douny C, Scippo ML, Delcenserie V. M-Batches to Simulate Luminal and Mucosal Human Gut Microbial Ecosystems: A Case Study of the Effects of Coffee and Green Tea. Microorganisms 2024; 12:236. [PMID: 38399640 PMCID: PMC10891782 DOI: 10.3390/microorganisms12020236] [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: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024] Open
Abstract
Gastrointestinal simulations in vitro have only limited approaches to analyze the microbial communities inhabiting the mucosal compartment. Understanding and differentiating gut microbial ecosystems is crucial for a more comprehensive and accurate representation of the gut microbiome and its interactions with the host. Herein is suggested, in a short-term and static set-up (named "M-batches"), the analysis of mucosal and luminal populations of inhabitants of the human colon. After varying several parameters, such as the fermentation volume and the fecal inoculum (single or pool), only minor differences in microbial composition and metabolic production were identified. However, the pool created with feces from five donors and cultivated in a smaller volume (300 mL) seemed to provide a more stable luminal ecosystem. The study of commercially available coffee and green tea in the M-batches suggested some positive effects of these worldwide known beverages, including the increase in butyrate-producing bacteria and lactobacilli populations. We hope that this novel strategy can contribute to future advances in the study of intestinal ecosystems and host-microbe relationships and help elucidate roles of the microbiome in health and disease.
Collapse
Affiliation(s)
- Elizabeth Goya-Jorge
- Laboratory of Food Quality Management, Department of Food Sciences, FARAH-Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium
- Intestinal Regenerative Medicine Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Irma Gonza
- Laboratory of Food Quality Management, Department of Food Sciences, FARAH-Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium
| | - Caroline Douny
- Laboratory of Food Analysis, Department of Food Sciences, FARAH-Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium
| | - Marie-Louise Scippo
- Laboratory of Food Analysis, Department of Food Sciences, FARAH-Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium
| | - Véronique Delcenserie
- Laboratory of Food Quality Management, Department of Food Sciences, FARAH-Veterinary Public Health, University of Liège, B43b, 4000 Liège, Belgium
| |
Collapse
|
36
|
Vacca M, Calabrese FM, Loperfido F, Maccarini B, Cerbo RM, Sommella E, Salviati E, Voto L, De Angelis M, Ceccarelli G, Di Napoli I, Raspini B, Porri D, Civardi E, Garofoli F, Campiglia P, Cena H, De Giuseppe R. Maternal Exposure to Endocrine-Disrupting Chemicals: Analysis of Their Impact on Infant Gut Microbiota Composition. Biomedicines 2024; 12:234. [PMID: 38275405 PMCID: PMC10813257 DOI: 10.3390/biomedicines12010234] [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: 12/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Endocrine disruptors (EDCs) are chemicals that interfere with the endocrine system. EDC exposure may contribute to the development of obesity, type 2 diabetes, and cardiovascular diseases by impacting the composition of an infant's gut microbiota during the first 1000 days of life. To explore the relationship between maternal urinary levels of Bisphenol-A and phthalates (UHPLC-MS/MS), and the composition of the infant gut microbiota (16S rDNA) at age 12 months (T3) and, retrospectively, at birth (T0), 1 month (T1), and 6 months (T2), stool samples from 20 infants breastfed at least once a day were analyzed. Metataxonomic bacteria relative abundances were correlated with EDC values. Based on median Bisphenol-A levels, infants were assigned to the over-exposed group (O, n = 8) and the low-exposed group (B, n = 12). The B-group exhibited higher gut colonization of the Ruminococcus torques group genus and the O-group showed higher abundances of Erysipelatoclostridium and Bifidobacterium breve. Additionally, infants were stratified as high-risk (HR, n = 12) or low-risk (LR, n = 8) exposure to phthalates, based on the presence of at least three phthalates with concentrations exceeding the cohort median values; no differences were observed in gut microbiota composition. A retrospective analysis of gut microbiota (T0-T2) revealed a disparity in β-diversity between the O-group and the B-group. Considering T0-T3, the Linear Discriminant Effect Size indicated differences in certain microbes between the O-group vs. the B-group and the HR-group vs. the LR-group. Our findings support the potential role of microbial communities as biomarkers for high EDC exposure levels. Nevertheless, further investigations are required to deeply investigate this issue.
Collapse
Affiliation(s)
- Mirco Vacca
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (M.V.); (F.M.C.); (M.D.A.)
| | - Francesco Maria Calabrese
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (M.V.); (F.M.C.); (M.D.A.)
| | - Federica Loperfido
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| | - Beatrice Maccarini
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| | - Rosa Maria Cerbo
- Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (R.M.C.); (E.C.); (F.G.)
| | - Eduardo Sommella
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.S.); (E.S.); (P.C.)
| | - Emanuela Salviati
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.S.); (E.S.); (P.C.)
| | - Luana Voto
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (M.V.); (F.M.C.); (M.D.A.)
| | - Gabriele Ceccarelli
- Human Anatomy Unit, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy;
| | - Ilaria Di Napoli
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| | - Benedetta Raspini
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| | - Debora Porri
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| | - Elisa Civardi
- Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (R.M.C.); (E.C.); (F.G.)
| | - Francesca Garofoli
- Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (R.M.C.); (E.C.); (F.G.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.S.); (E.S.); (P.C.)
| | - Hellas Cena
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
- Clinical Nutrition Unit, General Medicine, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy
| | - Rachele De Giuseppe
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy; (B.M.); (L.V.); (I.D.N.); (B.R.); (D.P.); (H.C.); (R.D.G.)
| |
Collapse
|
37
|
Doranga S, Krogfelt KA, Cohen PS, Conway T. Nutrition of Escherichia coli within the intestinal microbiome. EcoSal Plus 2024:eesp00062023. [PMID: 38417452 DOI: 10.1128/ecosalplus.esp-0006-2023] [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: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 03/01/2024]
Abstract
In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.
Collapse
Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen A Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark
| | - Paul S Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
38
|
Wang Y, Choo JM, Richard AC, Papanicolas LE, Wesselingh SL, Taylor SL, Rogers GB. Intestinal persistence of Bifidobacterium infantis is determined by interaction of host genetics and antibiotic exposure. THE ISME JOURNAL 2024; 18:wrae107. [PMID: 38896583 PMCID: PMC11214156 DOI: 10.1093/ismejo/wrae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/06/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024]
Abstract
Probiotics have gained significant attention as a potential strategy to improve health by modulating host-microbe interactions, particularly in situations where the normal microbiota has been disrupted. However, evidence regarding their efficacy has been inconsistent, with considerable interindividual variability in response. We aimed to explore whether a common genetic variant that affects the production of mucosal α(1,2)-fucosylated glycans, present in around 20% of the population, could explain the observed interpersonal differences in the persistence of commonly used probiotics. Using a mouse model with varying α(1,2)-fucosylated glycans secretion (Fut2WT or Fut2KO), we examined the abundance and persistence of Bifidobacterium strains (infantis, breve, and bifidum). We observed significant differences in baseline gut microbiota characteristics between Fut2WT and Fut2KO littermates, with Fut2WT mice exhibiting enrichment of species able to utilize α(1,2)-fucosylated glycans. Following antibiotic exposure, only Fut2WT animals showed persistent engraftment of Bifidobacterium infantis, a strain able to internalize α(1,2)-fucosylated glycans, whereas B. breve and B. bifidum, which cannot internalize α(1,2)-fucosylated glycans, did not exhibit this difference. In mice with an intact commensal microbiota, the relationship between secretor status and B. infantis persistence was reversed, with Fut2KO animals showing greater persistence compared to Fut2WT. Our findings suggest that the interplay between a common genetic variation and antibiotic exposure plays a crucial role in determining the dynamics of B. infantis in the recipient gut, which could potentially contribute to the observed variation in response to this commonly used probiotic species.
Collapse
Affiliation(s)
- Yiming Wang
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Jocelyn M Choo
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Alyson C Richard
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Lito E Papanicolas
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
- SA Pathology, SA Health, Adelaide, South Australia 5001, Australia
| | - Steve L Wesselingh
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
| | - Steven L Taylor
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5001, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| |
Collapse
|
39
|
Berberolli S, Wu M, Goycoolea FM. The Rosetta Stone of interactions of mucosa and associated bacteria in the gastrointestinal tract. Curr Opin Gastroenterol 2024; 40:1-6. [PMID: 37983559 PMCID: PMC10715687 DOI: 10.1097/mog.0000000000000992] [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] [Indexed: 11/22/2023]
Abstract
PURPOSE OF REVIEW Gut microbiota-mucosa-epithelial cells co-exist in an intricate three-way relationship that underpins gut homeostasis, and ultimately influences health and disease conditions. The O-glycans of mucin glycoproteins have been uncovered as a centrepiece of this system, although understanding the phenomena at play at the molecular level has been challenging and subject to significant traction over the last years. The purpose of this review is to discuss the recent advances in the phenomena that mediate microbiota and mucus multidirectional interactions in the human gut. RECENT FINDINGS The mucus biosynthesis and degradation by both commensal and pathogenic bacteria is under tight regulation and involves hundreds of carbohydrate-active enzymes (CAZy) and transporters. The fucosylation of O-glycans from mucin-2 seems to dictate binding by pathogenic species and to influence their virulence. Less clear is the influence of O-glycans in quorum sensing and biofilm formation. We have reviewed the advances in the in vitro models available to recreate the phenomena that capture the physiological context of the intestinal environment, emphasising models that include mucus and other aspects relevant to the physiological context. SUMMARY The recent findings highlight the importance of merging advances in analytical (glycans analysis) and omics techniques along with original robust in vitro models that enable to deconstruct part of the high complexity of the living gut and expand our understanding of the microbes-mucosa relationships and their significance in health and disease.
Collapse
Affiliation(s)
- Serena Berberolli
- School of Food Science and Nutrition, University of Leeds. Leeds, LS6 4RG, United Kingdom
| | | | | |
Collapse
|
40
|
Monshizadeh M, Ye Y. Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut Microbes 2024; 16:2302076. [PMID: 38214657 PMCID: PMC10793686 DOI: 10.1080/19490976.2024.2302076] [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: 05/17/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
We developed MicroKPNN, a prior-knowledge guided interpretable neural network for microbiome-based human host phenotype prediction. The prior knowledge used in MicroKPNN includes the metabolic activities of different bacterial species, phylogenetic relationships, and bacterial community structure, all in a shallow neural network. Application of MicroKPNN to seven gut microbiome datasets (involving five different human diseases including inflammatory bowel disease, type 2 diabetes, liver cirrhosis, colorectal cancer, and obesity) shows that incorporation of the prior knowledge helped improve the microbiome-based host phenotype prediction. MicroKPNN outperformed fully connected neural network-based approaches in all seven cases, with the most improvement of accuracy in the prediction of type 2 diabetes. MicroKPNN outperformed a recently developed deep-learning based approach DeepMicro, which selects the best combination of autoencoder and machine learning approach to make predictions, in all of the seven cases. Importantly, we showed that MicroKPNN provides a way for interpretation of the predictive models. Using importance scores estimated for the hidden nodes, MicroKPNN could provide explanations for prior research findings by highlighting the roles of specific microbiome components in phenotype predictions. In addition, it may suggest potential future research directions for studying the impacts of microbiome on host health and diseases. MicroKPNN is publicly available at https://github.com/mgtools/MicroKPNN.
Collapse
Affiliation(s)
- Mahsa Monshizadeh
- Computer Science Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- Computer Science Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| |
Collapse
|
41
|
Takada H, Katayama T, Katoh T. Cultivation of Microorganisms in Media Supplemented with Mucin Glycoproteins. Methods Mol Biol 2024; 2763:331-335. [PMID: 38347422 DOI: 10.1007/978-1-0716-3670-1_27] [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: 02/15/2024]
Abstract
To examine the mucin-utilizing capacity of bacterial isolates from fecal samples, an in vitro cultivation method using mucins as a carbon source should be considered. This chapter describes a practical method for cultivating bacteria in media containing mucin glycoproteins; for this cultivation method, several factors are considered due to the physical nature of mucin glycoproteins.
Collapse
Affiliation(s)
- Hiromi Takada
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| |
Collapse
|
42
|
Andreani NA, Sharma A, Dahmen B, Specht HE, Mannig N, Ruan V, Keller L, Baines JF, Herpertz-Dahlmann B, Dempfle A, Seitz J. Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome. Gut Microbes 2024; 16:2304158. [PMID: 38294867 PMCID: PMC10832965 DOI: 10.1080/19490976.2024.2304158] [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: 07/05/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
There is mounting evidence regarding the role of gut microbiota in anorexia nervosa (AN). Previous studies have reported that patients with AN show dysbiosis compared to healthy controls (HCs); however, the underlying mechanisms are unclear, and data on influencing factors and longitudinal course of microbiome changes are scarce. Here, we present longitudinal data of 57 adolescent inpatients diagnosed with AN at up to nine time points (including a 1-year follow-up examination) and compare these to up to six time points in 34 HCs. 16S rRNA gene sequencing was used to investigate the microbiome composition of fecal samples, and data on food intake, weight change, hormonal recovery (leptin levels), and clinical outcomes were recorded. Differences in microbiome composition compared to HCs were greatest during acute starvation and in the low-weight group, while diminishing with weight gain and especially weight recovery at the 1-year follow-up. Illness duration and prior weight loss were strongly associated with microbiome composition at hospital admission, whereas microbial changes during treatment were associated with kilocalories consumed, weight gain, and hormonal recovery. The microbiome at admission was prognostic for hospital readmission, and a higher abundance of Sutterella was associated with a higher body weight at the 1-year follow-up. Identifying these clinically important factors further underlines the potential relevance of gut microbial changes and may help elucidate the underlying pathophysiology of gut-brain interactions in AN. The characterization of prognostically relevant taxa could be useful to stratify patients at admission and to potentially identify candidate taxa for future supplementation studies aimed at improving AN treatment.
Collapse
Affiliation(s)
- Nadia Andrea Andreani
- Section of Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Arunabh Sharma
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Brigitte Dahmen
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Hannah E. Specht
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Nina Mannig
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Vanessa Ruan
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Lara Keller
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
43
|
Krigul KL, Feeney RH, Wongkuna S, Aasmets O, Holmberg SM, Andreson R, Puértolas-Balint F, Pantiukh K, Sootak L, Org T, Tenson T, Org E, Schroeder BO. A history of repeated antibiotic usage leads to microbiota-dependent mucus defects. Gut Microbes 2024; 16:2377570. [PMID: 39034613 DOI: 10.1080/19490976.2024.2377570] [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: 03/03/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.
Collapse
Affiliation(s)
- Kertu Liis Krigul
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Rachel H Feeney
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Supapit Wongkuna
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Oliver Aasmets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Sandra M Holmberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Reidar Andreson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Fabiola Puértolas-Balint
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Kateryna Pantiukh
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Linda Sootak
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tõnis Org
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Elin Org
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bjoern O Schroeder
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| |
Collapse
|
44
|
Conn KA, Borsom EM, Cope EK. Implications of microbe-derived ɣ-aminobutyric acid (GABA) in gut and brain barrier integrity and GABAergic signaling in Alzheimer's disease. Gut Microbes 2024; 16:2371950. [PMID: 39008552 PMCID: PMC11253888 DOI: 10.1080/19490976.2024.2371950] [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: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
The gut microbial ecosystem communicates bidirectionally with the brain in what is known as the gut-microbiome-brain axis. Bidirectional signaling occurs through several pathways including signaling via the vagus nerve, circulation of microbial metabolites, and immune activation. Alterations in the gut microbiota are implicated in Alzheimer's disease (AD), a progressive neurodegenerative disease. Perturbations in gut microbial communities may affect pathways within the gut-microbiome-brain axis through altered production of microbial metabolites including ɣ-aminobutyric acid (GABA), the primary inhibitory mammalian neurotransmitter. GABA has been shown to act on gut integrity through modulation of gut mucins and tight junction proteins and may be involved in vagus nerve signal inhibition. The GABAergic signaling pathway has been shown to be dysregulated in AD, and may be responsive to interventions. Gut microbial production of GABA is of recent interest in neurological disorders, including AD. Bacteroides and Lactic Acid Bacteria (LAB), including Lactobacillus, are predominant producers of GABA. This review highlights how temporal alterations in gut microbial communities associated with AD may affect the GABAergic signaling pathway, intestinal barrier integrity, and AD-associated inflammation.
Collapse
Affiliation(s)
- Kathryn A. Conn
- Center for Applied Microbiome Sciences, The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily M. Borsom
- Center for Data-Driven Discovery for Biology, Allen Institute, Seattle, WA, USA
| | - Emily K. Cope
- Center for Applied Microbiome Sciences, The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| |
Collapse
|
45
|
Zong W, Friedman ES, Allu SR, Firrman J, Tu V, Daniel SG, Bittinger K, Liu L, Vinogradov SA, Wu GD. Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome. Gut Microbes 2024; 16:2361493. [PMID: 38958039 PMCID: PMC11225921 DOI: 10.1080/19490976.2024.2361493] [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: 12/04/2023] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
The juxtaposition of well-oxygenated intestinal colonic tissue with an anerobic luminal environment supports a fundamentally important relationship that is altered in the setting of intestinal injury, a process likely to be relevant to diseases such as inflammatory bowel disease. Herein, using two-color phosphorometry to non-invasively quantify both intestinal tissue and luminal oxygenation in real time, we show that intestinal injury induced by DSS colitis reduces intestinal tissue oxygenation in a spatially defined manner and increases the flux of oxygen from the tissue into the gut lumen. By characterizing the composition of the microbiome in both DSS colitis-affected gut and in a bioreactor containing a stable human fecal community exposed to microaerobic conditions, we provide evidence that the increased flux of oxygen into the gut lumen augments glycan degrading bacterial taxa rich in glycoside hydrolases which are known to inhabit gut mucosal surface. Continued disruption of the intestinal mucus barrier through such a mechanism may play a role in the perpetuation of the intestinal inflammatory process.
Collapse
Affiliation(s)
- Wenjing Zong
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - Elliot S. Friedman
- Department of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Srinivasa Rao Allu
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Sergei A. Vinogradov
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary D. Wu
- Department of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
46
|
Aminov R, Aminova L. The role of the glycome in symbiotic host-microbe interactions. Glycobiology 2023; 33:1106-1116. [PMID: 37741057 PMCID: PMC10876039 DOI: 10.1093/glycob/cwad073] [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: 01/16/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 09/25/2023] Open
Abstract
Glycosylation plays a crucial role in many aspects of cell biology, including cellular and organismal integrity, structure-and-function of many glycosylated molecules in the cell, signal transduction, development, cancer, and in a number of diseases. Besides, at the inter-organismal level of interaction, a variety of glycosylated molecules are involved in the host-microbiota recognition and initiation of downstream signalling cascades depending on the outcomes of the glycome-mediated ascertainment. The role of glycosylation in host-microbe interactions is better elaborated within the context of virulence and pathogenicity in bacterial infection processes but the symbiotic host-microbe relationships also involve substantive glycome-mediated interactions. The works in the latter field have been reviewed to a much lesser extent, and the main aim of this mini-review is to compensate for this deficiency and summarise the role of glycomics in host-microbe symbiotic interactions.
Collapse
Affiliation(s)
- Rustam Aminov
- The School of Medicine, Medical Sciences and Nutrition, Foresterhill Campus, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - Leila Aminova
- Midwest Bioprocessing Center, 801 W Main St, Peoria, IL, 61606-1877, United States
| |
Collapse
|
47
|
Abstract
The amoeba parasite Entamoeba histolytica is the causative agent of human amebiasis, an enteropathic disease affecting millions of people worldwide. This ancient protozoan is an elementary example of how parasites evolve with humans, e.g. taking advantage of multiple mechanisms to evade immune responses, interacting with microbiota for nutritional and protective needs, utilizing host resources for growth, division, and encystation. These skills of E. histolytica perpetuate the species and incidence of infection. However, in 10% of infected cases, the parasite turns into a pathogen; the host-parasite equilibrium is then disorganized, and the simple lifecycle based on two cell forms, trophozoites and cysts, becomes unbalanced. Trophozoites acquire a virulent phenotype which, when non-controlled, leads to intestinal invasion with the onset of amoebiasis symptoms. Virulent E. histolytica must cross mucus, epithelium, connective tissue and possibly blood. This highly mobile parasite faces various stresses and a powerful host immune response, with oxidative stress being a challenge for its survival. New emerging research avenues and omics technologies target gene regulation to determine human or parasitic factors activated upon infection, their role in virulence activation, and in pathogenesis; this research bears in mind that E. histolytica is a resident of the complex intestinal ecosystem. The goal is to eradicate amoebiasis from the planet, but the parasitic life of E. histolytica is ancient and complex and will likely continue to evolve with humans. Advances in these topics are summarized here.
Collapse
Affiliation(s)
- Nancy Guillén
- Cell Biology and Infection Department, Institut Pasteur and Centre National de la Recherche Scientifique CNRS-ERM9195, Paris, France
| |
Collapse
|
48
|
Le D, Chambers MM, Mercado K, Gutowski CJ. Characterization of the gut microbiome in an osteosarcoma mouse model. J Orthop Res 2023; 41:2730-2739. [PMID: 37246455 DOI: 10.1002/jor.25635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023]
Abstract
Compelling evidence has mounted surrounding the relationship between the gut microbiome and many intestinal and extraintestinal cancers. Few studies exist investigating the relationship between the gut microbiome and sarcoma. We hypothesize that the presence of distant osteosarcoma induces change to the profile of flora within the mouse. Twelve mice were used for this experiment: six were sedated and received an injection of human osteosarcoma cells into the flank, while six served as controls. Baseline stool and weight were collected. Tumor size and mouse weight were recorded weekly, and stool samples were collected and stored. Fecal microbiomes of the mice were profiled by 16S rRNA gene sequencing and analyzed for alpha diversity, relative abundances of microbial taxa, and abundance of specific bacteria at different time points. Alpha diversity was increased in the osteosarcoma group compared with the control group. The family Lachnospiraceae had the second strongest negative net average change in relative abundance over time in the osteosarcoma group whereas it had a positive net average change in the control group. An increased Firmicutes/Bacteroidota (F/B) ratio was observed in the osteosarcoma group relative to the control mice. These differences suggest that there may be an interplay between the gut microbiome and osteosarcoma. Clinical significance: Due to the paucity of literature available, our work can support novel research on this relationship and the development of new, personalized treatments for osteosarcoma.
Collapse
Affiliation(s)
- David Le
- Department of Orthopaedic Surgery, Inspira Medical Center, Vineland, New Jersey, USA
| | | | - Kayla Mercado
- Department of Orthopaedic Surgery, Cooper University Healthcare, Camden, New Jersey, USA
| | - Christina J Gutowski
- Cooper Medical School of Rowan University, Camden, New Jersey, USA
- Department of Orthopaedic Surgery, Cooper University Healthcare, Camden, New Jersey, USA
| |
Collapse
|
49
|
Biţă CE, Scorei IR, Vreju AF, Muşetescu AE, Mogoşanu GD, Biţă A, Dinescu VC, Dinescu ŞC, Criveanu C, Bărbulescu AL, Florescu A, Ciurea PL. Microbiota-Accessible Boron-Containing Compounds in Complex Regional Pain Syndrome. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1965. [PMID: 38004014 PMCID: PMC10673453 DOI: 10.3390/medicina59111965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
The microbiota-gut-brain axis has garnered increasing attention in recent years for its role in various health conditions, including neuroinflammatory disorders like complex regional pain syndrome (CRPS). CRPS is a debilitating condition characterized by chronic neuropathic pain, and its etiology and pathophysiology remain elusive. Emerging research suggests that alterations in the gut microbiota composition and function could play a significant role in CRPS development and progression. Our paper explores the implications of microbiota in CRPS and the potential therapeutic role of boron (B). Studies have demonstrated that individuals with CRPS often exhibit dysbiosis, with imbalances in beneficial and pathogenic gut bacteria. Dysbiosis can lead to increased gut permeability and systemic inflammation, contributing to the chronic pain experienced in CRPS. B, an essential trace element, has shown promise in modulating the gut microbiome positively and exerting anti-inflammatory effects. Recent preclinical and clinical studies suggest that B supplementation may alleviate neuropathic pain and improve CRPS symptoms by restoring microbiota balance and reducing inflammation. Our review highlights the complex interplay between microbiota, inflammation, and neuropathic pain in CRPS and underscores the potential of B as a novel therapeutic approach to target the microbiota-gut-brain axis, offering hope for improved management of this challenging condition.
Collapse
Affiliation(s)
- Cristina Elena Biţă
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - Ion Romulus Scorei
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., 31B Dunării Street, 207465 Podari, Romania
| | - Ananu Florentin Vreju
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - Anca Emanuela Muşetescu
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - George Dan Mogoşanu
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (G.D.M.); (A.B.)
| | - Andrei Biţă
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (G.D.M.); (A.B.)
| | - Venera Cristina Dinescu
- Department of Health Promotion and Occupational Medicine, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania;
| | - Ştefan Cristian Dinescu
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - Cristina Criveanu
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - Andreea Lili Bărbulescu
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - Alesandra Florescu
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| | - Paulina Lucia Ciurea
- Department of Rheumatology, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania; (C.E.B.); (A.F.V.); (A.E.M.); (Ş.C.D.); (C.C.); (A.L.B.); (A.F.); (P.L.C.)
| |
Collapse
|
50
|
Sisk-Hackworth L, Brown J, Sau L, Levine AA, Tam LYI, Ramesh A, Shah RS, Kelley-Thackray ET, Wang S, Nguyen A, Kelley ST, Thackray VG. Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities. Biol Sex Differ 2023; 14:79. [PMID: 37932822 PMCID: PMC10626657 DOI: 10.1186/s13293-023-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine. METHODS We used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (n = 20) and male (n = 20) wild-type mice and female (n = 17) and male (n = 20) hypogonadal mice. RESULTS Both sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from the Bacteroidaceae, Eggerthellaceae, Muribaculaceae, and Rikenellaceae families, which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (Escherichia Shigella, Lachnoclostridium, and Eggerthellaceae genus) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine. CONCLUSIONS Our results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.
Collapse
Affiliation(s)
- Laura Sisk-Hackworth
- University of California San Diego, La Jolla, CA, USA
- San Diego State University, San Diego, CA, USA
| | - Jada Brown
- University of California San Diego, La Jolla, CA, USA
| | - Lillian Sau
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Reeya S Shah
- University of California San Diego, La Jolla, CA, USA
| | | | - Sophia Wang
- University of California San Diego, La Jolla, CA, USA
| | - Anita Nguyen
- University of California San Diego, La Jolla, CA, USA
| | | | | |
Collapse
|