1
|
Bajinka O, Darboe A, Tan Y, Abdelhalim KA, Cham LB. Gut microbiota and the human gut physiological changes. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01608-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
The human gut can be colonized by number of microorganisms. The most studied are bacteria, which changes from birth to newborn born into adult-like gut microbiota. Much is known about the effects of dietary, medications, and lifestyles on the bacterial composition. However, the host physiological changes influencing the gut microbiota, the immediate consequences, and the possible gut microbiota therapy are not studied at length. This review is based profoundly on animal model studies through experimentation and some human clinical trials for the past 20 years.
Forward
The physiological factors studied to influences gut microbiota are bacterial mucosal receptors, mucin glycosylation, mucus, epithelial microvilli, and tight junction. Host secretions and immune response such as immunity, secretory A (sIgA), inflammasome, innate immunity, immune response, glycans, bile acids, peristalsis, microRNA, and adhesion to intestinal glycans are as well found to confer variety of alterations on gut microbial flora.
Conclusion
Despite the resilience of the gut microbiota in response to changes, chain of events causes the imbalance microbiota. Increased pro-inflammatory potential with the help of cell barriers, host secretions, and immune response mediate gut recovery.
Collapse
|
2
|
Current understanding of the gut microbiota shaping mechanisms. J Biomed Sci 2019; 26:59. [PMID: 31434568 PMCID: PMC6702754 DOI: 10.1186/s12929-019-0554-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/14/2019] [Indexed: 12/14/2022] Open
Abstract
Increasing evidences have shown strong associations between gut microbiota and many human diseases, and understanding the dynamic crosstalks of host-microbe interaction in the gut has become necessary for the detection, prevention, or therapy of diseases. Many reports have showed that diet, nutrient, pharmacologic factors and many other stimuli play dominant roles in the modulation of gut microbial compositions. However, it is inappropriate to neglect the impact of host factors on shaping the gut microbiota. In this review, we highlighted the current findings of the host factors that could modulate the gut microbiota. Particularly the epithelium-associated factors, including the innate immune sensors, anti-microbial peptides, mucus barrier, secretory IgAs, epithelial microvilli, epithelial tight junctions, epithelium metabolism, oxygen barrier, and even the microRNAs are discussed in the context of the microbiota shaping. With these shaping factors, the gut epithelial cells could select the residing microbes and affect the microbial composition. This knowledge not only could provide the opportunities to better control many diseases, but may also be used for predicting the success of fecal microbiota transplantation clinically.
Collapse
|
3
|
Huang H, Krishnan HB, Pham Q, Yu LL, Wang TTY. Soy and Gut Microbiota: Interaction and Implication for Human Health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:8695-8709. [PMID: 27798832 DOI: 10.1021/acs.jafc.6b03725] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Soy (Glycine max) is a major commodity in the United States, and soy foods are gaining popularity due to their reported health-promoting effects. In the past two decades, soy and soy bioactive components have been studied for their health-promoting/disease-preventing activities and potential mechanisms of action. Recent studies have identified gut microbiota as an important component in the human body ecosystem and possibly a critical modulator of human health. Soy foods' interaction with the gut microbiota may critically influence many aspects of human development, physiology, immunity, and nutrition at different stages of life. This review summarizes current knowledge on the effects of soy foods and soy components on gut microbiota population and composition. It was found, although results vary in different studies, in general, both animal and human studies have shown that consumption of soy foods can increase the levels of bifidobacteria and lactobacilli and alter the ratio between Firmicutes and Bacteroidetes. These changes in microbiota are consistent with reported reductions in pathogenic bacteria populations in the gut, thereby lowering the risk of diseases and leading to beneficial effects on human health.
Collapse
Affiliation(s)
- Haiqiu Huang
- Diet, Genomics and Immunology Laboratory, U.S. Department of Agriculture-Agricultural Research Service , Beltsville, Maryland 20705, United States
| | - Hari B Krishnan
- Plant Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, University of Missouri , Columbia, Missouri 65211, United States
| | - Quynhchi Pham
- Diet, Genomics and Immunology Laboratory, U.S. Department of Agriculture-Agricultural Research Service , Beltsville, Maryland 20705, United States
| | - Liangli Lucy Yu
- Department of Nutrition and Food Science, University of Maryland , College Park, Maryland 20742, United States
| | - Thomas T Y Wang
- Diet, Genomics and Immunology Laboratory, U.S. Department of Agriculture-Agricultural Research Service , Beltsville, Maryland 20705, United States
| |
Collapse
|
4
|
Dimitriu PA, Boyce G, Samarakoon A, Hartmann M, Johnson P, Mohn WW. Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:200-10. [PMID: 23584963 DOI: 10.1111/j.1758-2229.2012.00393.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 08/17/2012] [Accepted: 08/28/2012] [Indexed: 05/20/2023]
Abstract
Gut microbial community properties of mammals are thought to be partly shaped by a combination of host immunity and environmental factors, but their relative importance is not firmly established. To address this gap, we first characterized the faecal bacteria of mice with a functioning immune system (wild-type, WT), mice with defective immune responses (CD45), mice lacking an adaptive immune system (RAG), and mice with both immune dysfunctions (45RAG). Using fingerprinting of 16S rRNA genes, we observed significant differences in gut microbiota composition across all mouse strains (P < 0.001) and identified several mouse strain-specific genera via pyrosequencing, including Turicibacter sp. (in WT mice) and Allobaculum sp. (in CD45-deficient animals). To define the role of the host immune system in constraining gut microbiota stability after perturbation, we cohoused CD45-deficient and WT mice and monitored gut bacterial community dynamics during 8 weeks. Cohousing caused the WT bacterial communities to become indistinguishable from those of CD45 mice (P > 0.05). Time-series analysis indicated that the communities of cohoused mice changed directionally as opposed to the relatively stable communities of non-cohoused controls. When we considered only taxonomic membership, it was the communities of CD45 non-cohoused mice that experienced the highest rate of change. Rather than be governed by fluctuations in the relative abundance of taxa, we suggest that CD45-regulated immune responses either are stimulated by the presence of bacteria per se or promote temporal stability by selecting for the occurrence of specific taxa.
Collapse
Affiliation(s)
- Pedro A Dimitriu
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | | | | | | | | | | |
Collapse
|
5
|
Hildebrand F, Nguyen TLA, Brinkman B, Yunta RG, Cauwe B, Vandenabeele P, Liston A, Raes J. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol 2013; 14:R4. [PMID: 23347395 PMCID: PMC4053703 DOI: 10.1186/gb-2013-14-1-r4] [Citation(s) in RCA: 335] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 01/08/2013] [Accepted: 01/24/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing. RESULTS We find initial evidence for richness-driven, strain-independent murine enterotypes that show a striking resemblance to those in human, and which associate with calprotectin levels, a marker for intestinal inflammation. After enterotype stratification, we find that genetic, caging and inter-individual variation contribute on average 19%, 31.7% and 45.5%, respectively, to the variance in the murine gut microbiota composition. Genetic distance correlates positively to microbiota distance, so that genetically similar strains have more similar microbiota than genetically distant ones. Specific mouse strains are enriched for specific operational taxonomic units and taxonomic groups, while the 'cage effect' can occur across mouse strain boundaries and is mainly driven by Helicobacter infections. CONCLUSIONS The detection of enterotypes suggests a common ecological cause, possibly low-grade inflammation that might drive differences among gut microbiota composition in mammals. Furthermore, the observed environmental and genetic effects have important consequences for experimental design in mouse microbiome research.
Collapse
Affiliation(s)
- Falk Hildebrand
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Thi Loan Anh Nguyen
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Autoimmune Genetics Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
- Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Brigitta Brinkman
- Department for Molecular Biomedical Research, VIB, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
- Department for Molecular Biomedical Research, GhentUniversity, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
| | - Roberto Garcia Yunta
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Benedicte Cauwe
- Autoimmune Genetics Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
- Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Peter Vandenabeele
- Department for Molecular Biomedical Research, VIB, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
- Department for Molecular Biomedical Research, GhentUniversity, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
| | - Adrian Liston
- Autoimmune Genetics Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
- Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jeroen Raes
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| |
Collapse
|
6
|
Keren N, Naftali T, Kovacs A, Konikoff FM, Gophna U. Can Colonoscopy Aspirates be a Substitute for Fecal Samples in Analyses of the Intestinal Microbiota? BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2012; 31:71-6. [PMID: 24936352 PMCID: PMC4034279 DOI: 10.12938/bmfh.31.71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/30/2012] [Indexed: 01/01/2023]
Abstract
There is a growing interest in the study of the human gut microbiota, as correlations between changes in bacterial profiles and diseases are increasingly discovered. Studies in this field generally use fecal samples, but it is often easier to obtain colon content aspirates during colonoscopy. This study used automated ribosomal internal spacer analysis (ARISA) to examine the extent to which the microbiota of colon aspirate samples obtained after bowel cleansing can reflect interindividual differences and serve as a proxy for fecal samples. Pre-bowel preparation fecal samples as well as colonoscopy aspirate samples from the cecum and rectum were obtained from 19 subjects. DNA was extracted from all samples, and comparative analysis was performed, including analysis of similarity (ANOSIM) and nonmetric multidimensional scaling. ANOSIM confirmed that samples from the same individual were well separated from samples from different individuals. Significantly larger differences were found between samples from different individuals than between samples of the same individual (R = 0.7605, p < 0.0001). These findings show that post-bowel preparation aspirates maintain a strong individual signature. Colonoscopy aspirates can therefore serve as a substitute for fecal samples in studies comparing the microbiota of different clinical study groups, especially when fecal samples are unavailable.
Collapse
Affiliation(s)
- Nirit Keren
- Department of Gastroenterology and Hepatology, Meir Medical Center, 59 Tshernichovsky St, Kfar Saba, 95847, Israel ; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Timna Naftali
- Department of Gastroenterology and Hepatology, Meir Medical Center, 59 Tshernichovsky St, Kfar Saba, 95847, Israel ; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Amir Kovacs
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Fred M Konikoff
- Department of Gastroenterology and Hepatology, Meir Medical Center, 59 Tshernichovsky St, Kfar Saba, 95847, Israel ; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| |
Collapse
|
7
|
Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 2011; 9:279-90. [PMID: 21407244 DOI: 10.1038/nrmicro2540] [Citation(s) in RCA: 984] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To what extent do host genetics control the composition of the gut microbiome? Studies comparing the gut microbiota in human twins and across inbred mouse lines have yielded inconsistent answers to this question. However, candidate gene approaches, in which one gene is deleted or added to a model host organism, show that a single host gene can have a tremendous effect on the diversity and population structure of the gut microbiota. Now, quantitative genetics is emerging as a highly promising approach that can be used to better understand the overall architecture of host genetic influence on the microbiota, and to discover additional host genes controlling microbial diversity in the gut. In this Review, we describe how host genetics and the environment shape the microbiota, and how these three factors may interact in the context of chronic disease.
Collapse
|
8
|
Kovacs A, Ben-Jacob N, Tayem H, Halperin E, Iraqi FA, Gophna U. Genotype is a stronger determinant than sex of the mouse gut microbiota. MICROBIAL ECOLOGY 2011; 61:423-8. [PMID: 21181142 DOI: 10.1007/s00248-010-9787-2] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Accepted: 12/03/2010] [Indexed: 05/09/2023]
Abstract
The mammalian gut microbiota is considered to be determined mostly by diet, while the effect of genotype is still controversial. Here, we examined the effect of genotype on the gut microbiota in normal populations, exhibiting only natural polymorphisms, and evaluated this effect in comparison to the effect of sex. DNA fingerprinting approaches were used to profile the gut microbiota of eight different recombinant inbred mouse lines of the collaborative cross consortium, whose level of genetic diversity mimics that of a natural human population. Analyses based on automated ribosomal internal transcribed spacer analysis demonstrated significant higher similarity of the gut microbiota composition within mouse lines than between them or within same-gender groups. Thus, genetic background significantly impacts the microbiota composition and is a stronger determinant than gender. These findings imply that genetic polymorphisms help shape the intestinal microbiota of mammals and consequently could affect host susceptibility to diseases.
Collapse
Affiliation(s)
- Amir Kovacs
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | | | | | | | | | | |
Collapse
|
9
|
Albert EJ, Duplisea J, Dawicki W, Haidl ID, Marshall JS. Tissue eosinophilia in a mouse model of colitis is highly dependent on TLR2 and independent of mast cells. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 178:150-60. [PMID: 21224053 DOI: 10.1016/j.ajpath.2010.11.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 07/22/2010] [Accepted: 09/09/2010] [Indexed: 12/20/2022]
Abstract
The mechanisms initiating eosinophil influx into sites of inflammation have been well studied in allergic disease but are poorly understood in other settings. This study examined the roles of TLR2 and mast cells in eosinophil accumulation during a nonallergic model of eosinophilia-associated colitis. TLR2-deficient mice (TLR2(-/-)) developed a more severe colitis than wild-type mice in the dextran sodium sulfate (DSS) model. However, they had significantly fewer eosinophils in the submucosa of the cecum (P < 0.01) and mid-colon (P < 0.01) than did wild-type mice after DSS treatment. Decreased eosinophilia in TLR2(-/-) mice was associated with lower levels of cecal CCL11 (P < 0.01). Peritoneal eosinophils did not express TLR2 protein, but TLR2 ligand injection into the peritoneal cavity induced local eosinophil recruitment, indicating that TLR2 activation of other cell types can mediate eosinophil recruitment. After DSS treatment, mast cell-deficient (Kit(W-sh/W-sh)) mice had similar levels of intestinal tissue eosinophilia were observed as those in wild-type mice. However, mast cell-deficient mice were partially protected from DSS-induced weight loss, an effect that was reversed by mast cell reconstitution. Overall, this study indicates a critical role for indirect TLR2-dependent pathways, but not mast cells, in the generation of eosinophilia in the large intestine during experimental colitis and has important implications for the regulation of eosinophils at mucosal inflammatory sites.
Collapse
Affiliation(s)
- Eric J Albert
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | | | | |
Collapse
|