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Beekman CN, Penumutchu S, Peterson R, Han G, Belenky M, Hasan MH, Belenky A, Beura LK, Belenky P. Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment. Cell Rep 2024; 43:114572. [PMID: 39116202 DOI: 10.1016/j.celrep.2024.114572] [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: 01/30/2024] [Revised: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Antibiotics cause collateral damage to resident microbes that is associated with various health risks. To date, studies have largely focused on the impacts of antibiotics on large intestinal and fecal microbiota. Here, we employ a gastrointestinal (GI) tract-wide integrated multiomic approach to show that amoxicillin (AMX) treatment reduces bacterial abundance, bile salt hydrolase activity, and unconjugated bile acids in the small intestine (SI). Losses of fatty acids (FAs) and increases in acylcarnitines in the large intestine (LI) correspond with spatially distinct expansions of Proteobacteria. Parasutterella excrementihominis engage in FA biosynthesis in the SI, while multiple Klebsiella species employ FA oxidation during expansion in the LI. We subsequently demonstrate that restoration of unconjugated bile acids can mitigate losses of commensals in the LI while also inhibiting the expansion of Proteobacteria during AMX treatment. These results suggest that the depletion of bile acids and lipids may contribute to AMX-induced dysbiosis in the lower GI tract.
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Affiliation(s)
- Chapman N Beekman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Rachel Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Geongoo Han
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Marina Belenky
- Felicitex Therapeutics Inc., 27 Strathmore Road, Natick, MA 01760, USA
| | - Mohammad H Hasan
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Alexei Belenky
- Felicitex Therapeutics Inc., 27 Strathmore Road, Natick, MA 01760, USA
| | - Lalit K Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
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Jiang C, Shi Y, Shi X, Yan J, Xuan L, Zhuang L, Li J, Xu G, Zheng J. ELOVL5 and VLDLR synergistically affect n-3 PUFA deposition in eggs of different chicken breeds. Poult Sci 2024; 103:104016. [PMID: 39018654 PMCID: PMC11287006 DOI: 10.1016/j.psj.2024.104016] [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: 04/08/2024] [Revised: 06/01/2024] [Accepted: 06/19/2024] [Indexed: 07/19/2024] Open
Abstract
There was no significant difference in the composition and content of fatty acids in eggs among different breeds initially, but following the supplementation of flaxseed oil, Dwarf Layer were observed to deposit more n-3 polyunsaturated fatty acid (PUFA) in eggs. Currently, there is limited research on the mechanisms underlying the differences in egg composition among different breeds. Therefore, in this study, 150 twenty-four-wk-old hens of each breed, including the Dwarf Layer and White Leghorn, were fed either a basal diet or a diet supplemented with 2.5% flaxseed oil. After 28 d, eggs and liver samples were collected to determine fatty acid composition, and serum, liver, intestine, and follicles were collected for subsequent biochemical, intestinal morphology, and lipid metabolism-related genes expression analysis. Duodenal contents were collected for microbial analysis. The results showed that there was no significant difference in the content and deposition efficiency of total n-3 PUFA in the liver of the 2 breeds, but the content and deposition efficiency of total n-3 PUFA in the egg of Dwarf Layer were significantly higher than those of White Leghorn after feeding flaxseed oil. Flaxseed oil and breeds did not have significant effects on cholesterol (CHO), free fatty acids (NEFA), low-density lipoprotein (LDL), and estrogen (E2) levels. After feeding with flaxseed oil, the villus height and the villus-to-crypt ratio in both breeds were increased and duodenal crypt depth was decreased. The villus-to-crypt ratio (4.78 vs. 3.60) in the duodenum of Dwarf Layer was significantly higher than that in White Leghorn after feeding with flaxseed oil. Flaxseed oil can impact the gut microbiota in the duodenum and reduce the microbiota associated with fatty acid breakdown, such as Romboutsia, Subdolibranulum, Lachnochlostridium, and Clostridium. This may mean that less ALA can be decomposed and more ALA can be absorbed into the body. Additionally, after feeding flaxseed oil, the mRNA levels of elongation enzymes 5 (ELOVL5), fatty acid desaturase 1 (FADS1), and fatty acid transporter 1 (FATP1) in the liver of Dwarf Layer were significantly higher than those in White Leghorn, while the mRNA levels of peroxisome proliferator-activated receptor alpha (PPAR), carnitine palmitoyl transferase 1 (CPT1), Acyl CoA oxidase 1 (ACOX1), and Acyl-CoA synthetase (ACSL) were significantly lower than those in White Leghorn. The mRNA level of FABP1 in the duodenum of Dwarf Layer was significantly higher than that of White Leghorn, while the mRNA level of FATP1 was significantly lower than that of White Leghorn. The protein levels of ELOVL5 in the liver of Dwarf Layer and very low-density lipoprotein receptor (VLDLR) in the follicles were significantly higher than those of White Leghorn. In summary, after feeding flaxseed oil, the higher ratio of villus height to crypt depth in Dwarf Layer allows more α-linolenic acid (ALA) to be absorbed into the body. The higher mRNA expression of FADS1, ELOVL5, and FATP1, as well as the higher protein expression of ELOVL5 in the liver of Dwarf Layer enhance the conversion of ALA into DHA. The higher protein expression of VLDLR in follicles of Dwarf Layer allows more n-3 PUFA to deposit in the follicles. These combined factors contribute to the Dwarf Layer's ability to deposit higher levels of n-3 PUFA in eggs, as well as improving the deposition efficiency of n-3 PUFA.
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Affiliation(s)
- Caiyun Jiang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuanhang Shi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Shi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jin Yan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Xuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Longyu Zhuang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guiyun Xu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Bendová B, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Piálek J, Schmiedová L, Kreisinger J. The strength of gut microbiota transfer along social networks and genealogical lineages in the house mouse. FEMS Microbiol Ecol 2024; 100:fiae075. [PMID: 38730559 PMCID: PMC11134300 DOI: 10.1093/femsec/fiae075] [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: 10/17/2023] [Revised: 02/23/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The gut microbiota of vertebrates is acquired from the environment and other individuals, including parents and unrelated conspecifics. In the laboratory mouse, a key animal model, inter-individual interactions are severely limited and its gut microbiota is abnormal. Surprisingly, our understanding of how inter-individual transmission impacts house mouse gut microbiota is solely derived from laboratory experiments. We investigated the effects of inter-individual transmission on gut microbiota in two subspecies of house mice (Mus musculus musculus and M. m. domesticus) raised in a semi-natural environment without social or mating restrictions. We assessed the correlation between microbiota composition (16S rRNA profiles), social contact intensity (microtransponder-based social networks), and mouse relatedness (microsatellite-based pedigrees). Inter-individual transmission had a greater impact on the lower gut (colon and cecum) than on the small intestine (ileum). In the lower gut, relatedness and social contact independently influenced microbiota similarity. Despite female-biased parental care, both parents exerted a similar influence on their offspring's microbiota, diminishing with the offspring's age in adulthood. Inter-individual transmission was more pronounced in M. m. domesticus, a subspecies, with a social and reproductive network divided into more closed modules. This suggests that the transmission magnitude depends on the social and genetic structure of the studied population.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | | | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Ľudovít Ďureje
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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Lo BC, Kryczek I, Yu J, Vatan L, Caruso R, Matsumoto M, Sato Y, Shaw MH, Inohara N, Xie Y, Lei YL, Zou W, Núñez G. Microbiota-dependent activation of CD4 + T cells induces CTLA-4 blockade-associated colitis via Fcγ receptors. Science 2024; 383:62-70. [PMID: 38175892 DOI: 10.1126/science.adh8342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024]
Abstract
Immune checkpoint inhibitors can stimulate antitumor immunity but can also induce toxicities termed immune-related adverse events (irAEs). Colitis is a common and severe irAE that can lead to treatment discontinuation. Mechanistic understanding of gut irAEs has been hampered because robust colitis is not observed in laboratory mice treated with checkpoint inhibitors. We report here that this limitation can be overcome by using mice harboring the microbiota of wild-caught mice, which develop overt colitis following treatment with anti-CTLA-4 antibodies. Intestinal inflammation is driven by unrestrained activation of IFNγ-producing CD4+ T cells and depletion of peripherally induced regulatory T cells through Fcγ receptor signaling. Accordingly, anti-CTLA-4 nanobodies that lack an Fc domain can promote antitumor responses without triggering colitis. This work suggests a strategy for mitigating gut irAEs while preserving antitumor stimulating effects of CTLA-4 blockade.
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Affiliation(s)
- Bernard C Lo
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roberta Caruso
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masanori Matsumoto
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yosuke Sato
- Takeda Pharmaceuticals International Co., Cambridge, MA 02139 USA
| | - Michael H Shaw
- Takeda Pharmaceuticals International Co., Cambridge, MA 02139 USA
| | - Naohiro Inohara
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuying Xie
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yu Leo Lei
- Department of Periodontics and Oral Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48104, USA
| | - Weiping Zou
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. mSystems 2023; 8:e0068823. [PMID: 37942948 PMCID: PMC10734470 DOI: 10.1128/msystems.00688-23] [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: 07/21/2023] [Accepted: 10/02/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE To our knowledge, IL-10-KO mice have not previously been used to investigate the interactions of host, microbiota, and broccoli, broccoli sprouts, or broccoli bioactives in resolving symptoms of CD. We showed that a diet containing 10% raw broccoli sprouts increased the plasma concentration of the anti-inflammatory compound sulforaphane and protected mice to varying degrees against disease symptoms, including weight loss or stagnation, fecal blood, and diarrhea. Younger mice responded more strongly to the diet, further reducing symptoms, as well as increased gut bacterial richness, increased bacterial community similarity to each other, and more location-specific communities than older mice on the diet intervention. Crohn's disease disrupts the lives of patients and requires people to alter dietary and lifestyle habits to manage symptoms. The current medical treatment is expensive with significant side effects, and a dietary intervention represents an affordable, accessible, and simple strategy to reduce the burden of symptoms.
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Affiliation(s)
- Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Brigitte Lavoie
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Jahnavi Pathak
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Gary M. Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Emma Perry
- Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Suzanne L. Ishaq
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Yanyan Li
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
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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.
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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
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Holman JM, Colucci L, Baudewyns D, Balkan J, Hunt T, Hunt B, Kinney M, Holcomb L, Stratigakis A, Chen G, Moses PL, Mawe GM, Zhang T, Li Y, Ishaq SL. Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice. mSystems 2023; 8:e0053223. [PMID: 37702510 PMCID: PMC10654075 DOI: 10.1128/msystems.00532-23] [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: 05/25/2023] [Accepted: 07/24/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE Evaluating bacterial communities across different locations in the gut provides a greater insight than fecal samples alone and provides an additional metric by which to evaluate beneficial host-microbe interactions. Here, we show that 10% steamed broccoli sprouts in the diet protects mice from the negative effects of dextran sodium sulfate-induced colitis, that colitis erases biogeographic patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. Mice fed the broccoli sprout diet during colitis performed better than mice fed the control diet while receiving DSS. The identification of accessible dietary components and concentrations that help maintain and correct the gut microbiome may provide universal and equitable approaches to IBD prevention and recovery, and broccoli sprouts represent a promising strategy.
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Affiliation(s)
- Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA
| | - Dorien Baudewyns
- Department of Psychology, University of Maine, Orono, Maine, USA
| | - Joe Balkan
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter L. Moses
- Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Gary M. Mawe
- Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Yanyan Li
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Suzanne L. Ishaq
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
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8
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Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525953. [PMID: 36747766 PMCID: PMC9900910 DOI: 10.1101/2023.01.27.525953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Crohn's Disease (CD) is a presentation of Inflammatory Bowel Disease (IBD) that manifests in childhood and adolescence, and involves chronic and severe enterocolitis, immune and gut microbiome dysregulation, and other complications. Diet and gut-microbiota-produced metabolites are sources of anti-inflammatories which could ameliorate symptoms. However, questions remain on how IBD influences biogeographic patterns of microbial location and function in the gut, how early life transitional gut communities are affected by IBD and diet interventions, and how disruption to biogeography alters disease mediation by diet components or microbial metabolites. Many studies on diet and IBD use a chemically induced ulcerative colitis model, despite the availability of an immune-modulated CD model. Interleukin-10-knockout (IL-10-KO) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed a control diet or one containing 10% (w/w) raw broccoli sprouts, which was high in the sprout-sourced anti-inflammatory sulforaphane. Diets began 7 days prior to, and for 2 weeks after inoculation with Helicobacter hepaticus, which triggers Crohn's-like symptoms in these immune-impaired mice. The broccoli sprout diet increased sulforaphane in plasma; decreased weight stagnation, fecal blood, and diarrhea associated; and increased microbiota richness in the gut, especially in younger mice. Sprout diets resulted in some anatomically specific bacteria in younger mice, and reduced the prevalence and abundance of pathobiont bacteria which trigger inflammation in the IL-10-KO mouse, for example; Escherichia coli and Helicobacter. Overall, the IL-10-KO mouse model is responsive to a raw broccoli sprout diet and represents an opportunity for more diet-host-microbiome research.
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Affiliation(s)
- Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Brigitte Lavoie
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA 04401
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Jahnavi Pathak
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Gary M. Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
- Finch Therapeutics, Somerville, Massachusetts, USA 02143
| | - Emma Perry
- Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA 04469
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109
| | - Suzanne L. Ishaq
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Yanyan Li
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
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Holman JM, Colucci L, Baudewyns D, Balkan J, Hunt T, Hunt B, Kinney M, Holcomb L, Chen G, Moses PL, Mawe GM, Zhang T, Li Y, Ishaq SL. Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.522641. [PMID: 37292900 PMCID: PMC10245759 DOI: 10.1101/2023.01.27.522641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, and affordable, for managing symptoms. Glucosinolate compounds are highly concentrated in broccoli sprouts, especially glucoraphanin, and can be metabolized by certain mammalian gut bacteria into anti inflammatory isothiocyanates, such as sulforaphane. Gut microbiota exhibit biogeographic patterns, but it is unknown if colitis alters these or whether the location of glucoraphanin metabolizing bacteria affects anti-inflammatory benefits. We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 34-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, lipocalin, serum cytokines, and bacterial communities from the luminal and mucosa-associated populations in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet with DSS treatment performed better than mice fed the control diet with DSS, including significantly more weight gain, lower Disease Activity Indexes, lower plasma lipocalin and proinflammatory cytokines, and higher bacterial richness in all gut locations. Bacterial communities were assorted by gut location, but were more homogenous across locations in the control diet + DSS mice. Importantly, our results showed that broccoli sprout feeding abrogated the effects of DSS on gut microbiota, as bacterial richness and biogeography were similar between mice receiving broccoli sprouts with and without DSS. Collectively, these results support the protective effect of steamed broccoli sprouts against dysbiosis and colitis induced by DSS. Importance Evaluating bacterial communities across different locations in the gut provides a greater insight than fecal samples alone, and provides an additional metric by which to evaluate beneficial host-microbe interactions. Here, we show that 10% steamed broccoli sprouts in the diet protects mice from the negative effects of dextran sodium sulfate induced colitis, that colitis erases biogeographical patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. Mice fed the broccoli sprout diet during colitis performed better than mice fed the control diet while receiving DSS. The identification of accessible dietary components and concentrations that help maintain and correct the gut microbiome may provide universal and equitable approaches to IBD prevention and recovery, and broccoli sprouts represent a promising strategy.
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Affiliation(s)
- Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA 04401
| | | | - Joe Balkan
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA 02155
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109
| | - Peter L. Moses
- Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
- Finch Therapeutics, Somerville, Massachusetts, USA 02143
| | - Gary M. Mawe
- Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Yanyan Li
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Suzanne L. Ishaq
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
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10
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Neha SA, Salazar-Bravo J. Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus). BMC Microbiol 2023; 23:51. [PMID: 36858951 PMCID: PMC9979494 DOI: 10.1186/s12866-023-02778-0] [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: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing. RESULTS The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity. CONCLUSIONS Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.
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Affiliation(s)
- Sufia Akter Neha
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA.
| | - Jorge Salazar-Bravo
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA
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11
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Shang Y, Zhong H, Liu G, Wang X, Wu X, Wei Q, Shi L, Zhang H. Characteristics of Microbiota in Different Segments of the Digestive Tract of Lycodon rufozonatus. Animals (Basel) 2023; 13:ani13040731. [PMID: 36830518 PMCID: PMC9952230 DOI: 10.3390/ani13040731] [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: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of Lycodon rufozonatus. Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the L. rufozonatus gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.
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Affiliation(s)
- Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Huaming Zhong
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China
| | - Gang Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence:
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12
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Yan G, Li S, Wen Y, Luo Y, Huang J, Chen B, Lv S, Chen L, He L, He M, Yang Q, Yu Z, Xiao W, Tang Y, Li W, Han J, Zhao F, Yu S, Kong F, Abbasi B, Yin H, Gu C. Characteristics of intestinal microbiota in C57BL/6 mice with non-alcoholic fatty liver induced by high-fat diet. Front Microbiol 2022; 13:1051200. [PMID: 36620001 PMCID: PMC9813237 DOI: 10.3389/fmicb.2022.1051200] [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: 09/22/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction As a representation of the gut microbiota, fecal and cecal samples are most often used in human and animal studies, including in non-alcoholic fatty liver disease (NAFLD) research. However, due to the regional structure and function of intestinal microbiota, whether it is representative to use cecal or fecal contents to study intestinal microbiota in the study of NAFLD remains to be shown. Methods The NAFLD mouse model was established by high-fat diet induction, and the contents of the jejunum, ileum, cecum, and colon (formed fecal balls) were collected for 16S rRNA gene analysis. Results Compared with normal mice, the diversity and the relative abundance of major bacteria and functional genes of the ileum, cecum and colon were significantly changed, but not in the jejunum. In NAFLD mice, the variation characteristics of microbiota in the cecum and colon (feces) were similar. However, the variation characteristics of intestinal microbiota in the ileum and large intestine segments (cecum and colon) were quite different. Discussion Therefore, the study results of cecal and colonic (fecal) microbiota cannot completely represent the results of jejunal and ileal microbiota.
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Affiliation(s)
- Guangwen Yan
- College of Animal Science, Xichang University, Xichang, China
| | - Shuaibing Li
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Yuhang Wen
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Yadan Luo
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Jingrong Huang
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Baoting Chen
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Shuya Lv
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Lang Chen
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Lvqin He
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Manli He
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Qian Yang
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Zehui Yu
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Wudian Xiao
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Yong Tang
- Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Weiyao Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jianhong Han
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Fangfang Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shumin Yu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Fang Kong
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Benazir Abbasi
- College of Veterinary Medicine, Nanjing Agricultural University, Jiangsu, China
| | - Hongmei Yin
- College of Animal Science, Xichang University, Xichang, China,*Correspondence: Hongmei Yin,
| | - Congwei Gu
- Laboratory Animal Centre, Southwest Medical University, Luzhou, China,Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China,College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Congwei Gu,
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13
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Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity. COMMUNICATIONS MEDICINE 2022; 2:127. [PMID: 36217535 PMCID: PMC9546886 DOI: 10.1038/s43856-022-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
Background Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated. Methods To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D (n = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; n = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level. Results Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control. Conclusion We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality. Weight-loss surgery is a highly effective treatment of type 2 diabetes in people with obesity. Interestingly, the improvement in diabetes after weight-loss surgery occurs before any significant weight-loss. Through better understanding of this metabolic improvement, weight-loss surgery provides a unique avenue to identify novel ways of treating diabetes and obesity. Here we combine measurements of metabolism, gut bacteria and diet in people with obesity, with or without type 2 diabetes and in patients before and after weight-loss surgery. We have used these data to identify changes associated with weight-loss surgery, obesity and diabetes. Improved understanding of the mechanisms behind these changes, including how changes to gut bacteria influence metabolism, may lead to new treatments for weight-loss or diabetes. Penney et al. conduct microbial and metabolic profiling in people with obesity, with or without type 2 diabetes, undergoing two types of bariatric surgery. Integrative analysis identifies multi-omic signatures associated with response to surgery, body mass index, and glycaemic control.
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14
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Periodical Changes of Feces Microbiota and Its Relationship with Nutrient Digestibility in Early Lambs. Animals (Basel) 2022; 12:ani12141770. [PMID: 35883317 PMCID: PMC9311505 DOI: 10.3390/ani12141770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Early mammal gut microorganism colonization affects host health, the feed conversion rate, and production performance. Herein, we explored how fecal microbiota develops and the interactions between microorganisms and nutrients. The lambs were separated from ewes at 7 days old, artificial feeding with milk replacer completely replaced lactation, and the starter diet was added. At 21 days old, the lambs were fed with complete starter and milk replacer was stopped. At day 7, 21, 35, and 49 after birth, fecal samples were collected. Then 16S rRNA gene sequencing in the fecal samples revealed that the alpha diversity increased significantly with age. Principal coordinates analysis showed clear clustering by age (p < 0.05). At the genus level, the relative abundance of 8 genera declined, 12 genera increased (p < 0.1), and 4 genera changed dramatically with age (p < 0.05). The apparent digestibility of dry matter, protein, fat, neutral detergent fiber, and acid detergent fiber significantly decreased by 21.77%, 23.15%, 23.62%, 19.38%, and 45.24%, respectively, from 7 to 35 days of age (p < 0.05), but not thereafter (p > 0.05). Fecal nutrient contents affected the abundance of bacterial genera (p < 0.05). Enterobacteriaceae_unclassified, Clostridium XlVb, Bifidobacterium, and other genera had no relationship with the fecal nutrient content; however, they were closely related to nutrient intake and digestibility, possibly promoting nutrient digestion. Our results suggested that nutrient digestion of young lambs changed rapidly, which was closely related to intestinal microbial colonization.
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15
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Bendová B, Mikula O, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Martin JF, Piálek J, Schmiedová L, Kreisinger J. Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions. FEMS Microbiol Ecol 2022; 98:6620832. [PMID: 35767862 DOI: 10.1093/femsec/fiac078] [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: 12/03/2021] [Revised: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are therefore an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under semi-natural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of co-divergence with their hosts. Helicobacters represent promising candidates for studying GM-host co-adaptations and the fitness effects of their interactions.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ondřej Mikula
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Dagmar Čížková
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Jaroslav Piálek
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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16
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ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 2022; 606:358-367. [PMID: 35477154 PMCID: PMC9157047 DOI: 10.1038/s41586-022-04769-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
Abstract
The composition of the intestinal microbiome varies considerably between individuals and is correlated with health1. Understanding the extent to which, and how, host genetics contributes to this variation is essential yet has proved to be difficult, as few associations have been replicated, particularly in humans2. Here we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N-acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N-acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N-acetyl-galactosamine. Our results provide very strong evidence for an effect of the host genotype on the abundance of specific bacteria in the intestine combined with insights into the molecular mechanisms that underpin this association. Our data pave the way towards identifying the same effect in rural human populations. The host blood-type-associated ABO genotype affects the abundance of specific bacteria in the pig intestine.
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17
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Kohl KD, Dieppa-Colón E, Goyco-Blas J, Peralta-Martínez K, Scafidi L, Shah S, Zawacki E, Barts N, Ahn Y, Hedayati S, Secor SM, Rowe MP. Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies. Integr Comp Biol 2022; 62:237-251. [PMID: 35587374 DOI: 10.1093/icb/icac045] [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: 03/01/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus), and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus) capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Etan Dieppa-Colón
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260.,Department of Bacteriology, University of Wisconsin - Madison, Madison WI 53706
| | - José Goyco-Blas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | | | - Luke Scafidi
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Sarth Shah
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Emma Zawacki
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Nick Barts
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Young Ahn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Stefanie Hedayati
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Stephen M Secor
- Department of Biological Sciences, University of Alabama, Tuscaloosa AL 35487
| | - Matthew P Rowe
- Department of Biological Sciences, University of Oklahoma, Norman OK 73019
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18
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Moore NB, Stephens RB, Rowe RJ. Nutritional and environmental factors influence small mammal seed selection in a northern temperate forest. Ecosphere 2022. [DOI: 10.1002/ecs2.4036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Nicholas B. Moore
- Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
| | - Ryan B. Stephens
- Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
| | - Rebecca J. Rowe
- Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
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19
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Gu M, Samuelson DR, de la Rua NM, Charles TP, Taylor CM, Luo M, Siggins RW, Shellito JE, Welsh DA. Host innate and adaptive immunity shapes the gut microbiota biogeography. Microbiol Immunol 2022; 66:330-341. [PMID: 35067963 DOI: 10.1111/1348-0421.12963] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
The gut microbiota has a fundamental role in the development and the maturation of the host immune system. Both innate and adaptive immune cells have critical functions in microbial pathogen containment and clearance, but the regulation of the commensal microbiome ecosystem in the gastrointestinal tract by these major immune cell populations is incompletely defined. We investigated the role of specific innate and adaptive immune cell in the regulation of the microbiota in the intestinal tract biogeographically. Dendritic cells, macrophages, CD4+ T-cells, CD8+ T-cells, and B-cells were depleted using monoclonal antibodies and clodronate liposomes, and the microbial communities was determined by 16S rRNA gene sequencing. With specific immune cell depletion, distinct microbiota changes were observed. In general, immune cell depleted mice had higher microbiota richness and evenness at all gut anatomical sites. At each gut segment, samples from immune cell-depleted animals clustered away from the Isotype/Liposome control mice. This was especially dramatic for small intestinal microbiota. Specifically, Enterobacteriaceae, Bacteroides acidifaciens and Mucispirillum schaedleri were highly enriched in the mucosa and lumen of the small intestine in immune cell-deficient animals. Further, the mucosal microbiota had higher microbiota evenness compared to luminal microbiota at all gut segments, and the UniFrac distance between B cell depleted and isotype control mice was the largest in duodenum followed by ileum and colon. Taken together, our data suggest that innate and adaptive immune cells specifically contribute to the regulation of the gut microbiota's biogeographical distribution along the gastrointestinal tract, and microbiota in duodenum mucosa are more responsive to host immune changes compared to other anatomical sites. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Min Gu
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Derrick R Samuelson
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Internal Medicine, Division of Pulmonary, Critical Care, & Sleep, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicholas M de la Rua
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Tysheena P Charles
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Meng Luo
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Robert W Siggins
- Department of Physiology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Judd E Shellito
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - David A Welsh
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
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20
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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21
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Anders JL, Moustafa MAM, Mohamed WMA, Hayakawa T, Nakao R, Koizumi I. Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents. Sci Rep 2021; 11:19929. [PMID: 34620922 PMCID: PMC8497572 DOI: 10.1038/s41598-021-99379-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023] Open
Abstract
Host-microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.
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Affiliation(s)
- Jason L. Anders
- grid.39158.360000 0001 2173 7691Graduate School of Environmental Science, Hokkaido University, N10W5, Sapporo, Hokkaido 060-0810 Japan
| | - Mohamed Abdallah Mohamed Moustafa
- grid.39158.360000 0001 2173 7691Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Sapporo, Hokkaido 060-0818 Japan ,grid.412707.70000 0004 0621 7833Department Animal Medicine, South Valley University, Qena, 83523 Egypt
| | - Wessam Mohamed Ahmed Mohamed
- grid.39158.360000 0001 2173 7691Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Sapporo, Hokkaido 060-0818 Japan
| | - Takashi Hayakawa
- grid.39158.360000 0001 2173 7691Faculty of Environmental Earth Science, Hokkaido University, N10W5, Sapporo, Hokkaido 060-0810 Japan ,grid.471626.00000 0004 4649 1909Japan Monkey Centre, Inuyama, Aichi 484-0081 Japan
| | - Ryo Nakao
- grid.39158.360000 0001 2173 7691Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Sapporo, Hokkaido 060-0818 Japan
| | - Itsuro Koizumi
- grid.39158.360000 0001 2173 7691Faculty of Environmental Earth Science, Hokkaido University, N10W5, Sapporo, Hokkaido 060-0810 Japan
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22
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Montenegro-Burke JR, Kok BP, Guijas C, Domingo-Almenara X, Moon C, Galmozzi A, Kitamura S, Eckmann L, Saez E, Siuzdak GE, Wolan DW. Metabolomics activity screening of T cell-induced colitis reveals anti-inflammatory metabolites. Sci Signal 2021; 14:eabf6584. [PMID: 34582249 DOI: 10.1126/scisignal.abf6584] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- J Rafael Montenegro-Burke
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Bernard P Kok
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Carlos Guijas
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Xavier Domingo-Almenara
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Clara Moon
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrea Galmozzi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Seiya Kitamura
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lars Eckmann
- Department of Medicine, University of California, La Jolla CA 92093, USA
| | - Enrique Saez
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gary E Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA.,Department of Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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23
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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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24
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Abstract
Laboratory mice have long been an invaluable tool in biomedical science and have made significant contributions in research into life-threatening diseases. However, the translation of research results from mice to humans often proves difficult due to the incomplete nature of laboratory animal-based research. Hence, there is increasing demand for complementary methods or alternatives to laboratory mice that can better mimic human physiological traits and potentially bridge the translational research gap. Under these circumstances, the natural/naturalized mice including “wild”, “dirty”, “wildling”, and “wilded” systems have been found to better reflect some aspects of human pathophysiology. Here, we discuss the pros and cons of the laboratory mouse system and contemplate how wild mice and wild microbiota are able to help in refining such systems to better mimic the real-world situation and contribute to more productive translational research.
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Affiliation(s)
- Ho-Keun Kwon
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases and Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, South Korea.
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826, South Korea.
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25
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Low A, Soh M, Miyake S, Aw VZJ, Feng J, Wong A, Seedorf H. Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract. Int J Mol Sci 2021; 22:5981. [PMID: 34205981 PMCID: PMC8198505 DOI: 10.3390/ijms22115981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 01/04/2023] Open
Abstract
Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance of expanding sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.
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Affiliation(s)
- Adrian Low
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Sou Miyake
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Vanessa Zhi Jie Aw
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Jian Feng
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Adeline Wong
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
- Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
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26
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Adade EE, Al Lakhen K, Lemus AA, Valm AM. Recent progress in analyzing the spatial structure of the human microbiome: distinguishing biogeography and architecture in the oral and gut communities. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2021; 18:275-283. [PMID: 35936977 PMCID: PMC9351436 DOI: 10.1016/j.coemr.2021.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fueled by technological advances in methods for sample collection and preservation in sequencing studies, and in advances in computational analyses of high content image data, the spatial structure of the human microbiome is coming to light. In this mini-review, we summarize recent developments in our understanding of the structure of two human microbiomes: the lower gut and the oral cavity. We focus on only the most recent literature and we make an important distinction between two forms of spatial structure, governed by scale: biogeography and architecture. By segmenting the study of microbiome spatial structure into two categories, we demonstrate the potential to greatly advance our understanding of the mechanistic principles that link structure and function in the microbiome.
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Affiliation(s)
- Emmanuel E. Adade
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA
| | - Khalid Al Lakhen
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA
| | - Alex A. Lemus
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA
| | - Alex M. Valm
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA,Corresponding author.
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27
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Lu C, Tang S, Han J, Fan S, Huang Y, Zhang Z, Zhou J, Ming T, Li Y, Su X. Apostichopus japonicus Oligopeptide Induced Heterogeneity in the Gastrointestinal Tract Microbiota and Alleviated Hyperuricemia in a Microbiota-Dependent Manner. Mol Nutr Food Res 2021; 65:e2100147. [PMID: 34018696 DOI: 10.1002/mnfr.202100147] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/22/2021] [Indexed: 12/13/2022]
Abstract
SCOPE This study aims to investigate the protective effect of Apostichopus japonicus oligopeptide (AJOP) on hyperuricemia, demonstrate the modulation of the gastrointestinal tract (GIT) microbiota, and clarify the underlying microbiota-dependent mechanism. METHODS AND RESULTS Hyperuricemic mice treated with AJOP and subjected to corresponding fecal microbiota transplantation (FMT) are used to observe the beneficial effects of AJOP and microbiota. Gene transcriptions are measured using quantitative real-time PCR. The GIT (stomach, colon, cecum, and feces) microbiota is analyzed by 16S rDNA sequencing and the short-chain fatty acids are detected using GC-MS. Dietary administration of AJOP significantly alleviates hyperuricemia, regulates uric acid metabolism, inhibites the activation of the NLRP3 inflammasome and NF-κB-related signaling pathway, and restores m6A methylation levels. In addition, substantial heterogeneity is observed in GIT microbiota. Furthermore, FMT effectively alleviates hyperuricemia in mice by selectively regulating the corresponding pathways associated with AJOP treatment, indicating that the mechanism underlying the protective effects of AJOP is partly microbiota-dependent. CONCLUSION This study demonstrates that AJOP exerts a protective effect on hyperuricemic mice by regulating uric acid metabolism, resulting in substantial heterogeneity among the GIT microbiota, thus mediating the beneficial effects in a microbiota-dependent manner.
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Affiliation(s)
- Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 169 Qixing South Road, Ningbo, China.,School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Shasha Tang
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 169 Qixing South Road, Ningbo, China.,School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Siqing Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 169 Qixing South Road, Ningbo, China.,School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Yumeng Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 169 Qixing South Road, Ningbo, China.,School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Zhen Zhang
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 169 Qixing South Road, Ningbo, China.,School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Tinghong Ming
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Ye Li
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 169 Qixing South Road, Ningbo, China.,School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
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28
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Guerre P. Mycotoxin and Gut Microbiota Interactions. Toxins (Basel) 2020; 12:E769. [PMID: 33291716 PMCID: PMC7761905 DOI: 10.3390/toxins12120769] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
The interactions between mycotoxins and gut microbiota were discovered early in animals and explained part of the differences in susceptibility to mycotoxins among species. Isolation of microbes present in the gut responsible for biotransformation of mycotoxins into less toxic metabolites and for binding mycotoxins led to the development of probiotics, enzymes, and cell extracts that are used to prevent mycotoxin toxicity in animals. More recently, bioactivation of mycotoxins into toxic compounds, notably through the hydrolysis of masked mycotoxins, revealed that the health benefits of the effect of the gut microbiota on mycotoxins can vary strongly depending on the mycotoxin and the microbe concerned. Interactions between mycotoxins and gut microbiota can also be observed through the effect of mycotoxins on the gut microbiota. Changes of gut microbiota secondary to mycotoxin exposure may be the consequence of the antimicrobial properties of mycotoxins or the toxic effect of mycotoxins on epithelial and immune cells in the gut, and liberation of antimicrobial peptides by these cells. Whatever the mechanism involved, exposure to mycotoxins leads to changes in the gut microbiota composition at the phylum, genus, and species level. These changes can lead to disruption of the gut barrier function and bacterial translocation. Changes in the gut microbiota composition can also modulate the toxicity of toxic compounds, such as bacterial toxins and of mycotoxins themselves. A last consequence for health of the change in the gut microbiota secondary to exposure to mycotoxins is suspected through variations observed in the amount and composition of the volatile fatty acids and sphingolipids that are normally present in the digesta, and that can contribute to the occurrence of chronic diseases in human. The purpose of this work is to review what is known about mycotoxin and gut microbiota interactions, the mechanisms involved in these interactions, and their practical application, and to identify knowledge gaps and future research needs.
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Affiliation(s)
- Philippe Guerre
- Ecole Nationale Vétérinaire de Toulouse, Université de Toulouse, ENVT, F-31076 Toulouse, France
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29
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Ding C, Yang D, Ma J, Jin M, Shen Z, Shi D, Tian Z, Kang M, Li J, Qiu Z. Effects of free antibiotic resistance genes in the environment on intestinal microecology of mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111119. [PMID: 32798757 DOI: 10.1016/j.ecoenv.2020.111119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
The rapid spread of antibiotic resistance genes (ARGs) is a great challenge to the ecological safety and human health. The intestine of humans and animals is an important site for the increase and spread of ARGs due to the great diversity and abundance of microorganisms in the intestinal microecology. ARGs, including the intracellular (iARGs) and the extracellular (eARGs) ARGs, are usually introduced into the intestinal tract through the diet, and the iARGs are colonized and spread in the intestinal microbiota with the help of the host bacteria. However, whether the eARGs can enter the intestinal microorganisms in the absence of host bacteria is not known. Here, we show the transformation and the diffusion of the ampramycin resistance gene (Ap) carried by the free plasmid RK2 in the intestinal microbiota of mice. After two days of consecutive gavage with free RK2, the intracellular Ap gene increases from days 0-8 in the feces of mice, and has remained constant. Bacterial transformation happens in the small intestine, including proximal and distal jejuna and proximal and distal ilea, at the early stage (first two days), and the intracellular RK2 is diffused into the intestinal microbiota of mice by conjugation on days 2-8 day, which is based on the distribution of eARG and iARG and the mRNA expression levels of trbBp, trfAp, korA, korB, and trbA. The characteristics of ARGs susceptible microbiota for transformation are analyzed using 16s rRNA gene sequencing, transmission electron microscopy, and flow cytometric. The ingestion of RK2 affects the composition of intestinal microbiota especially for Proteobacteria, and the antibiotic residue promotes the increase in Escherichia coli. These findings are important to assess the risk of ARGs, especially the eARGs in the intestinal microecology.
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Affiliation(s)
- Chengshi Ding
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China; College of Life Science, Zaozhuang University, Zaozhuang, 277160, China
| | - Dong Yang
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China
| | - Jing Ma
- College of Life Science, Zaozhuang University, Zaozhuang, 277160, China
| | - Min Jin
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China
| | - Zhiqiang Shen
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China
| | - Danyang Shi
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China
| | - Zhongjing Tian
- College of Life Science, Zaozhuang University, Zaozhuang, 277160, China
| | - Meiling Kang
- College of Life Science, Zaozhuang University, Zaozhuang, 277160, China
| | - Junwen Li
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China.
| | - Zhigang Qiu
- Tianjin Institute of Environmental Medicine and Operational Medicine, Tianjin, 300050, China.
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Ishikawa T, Omori T, Kikuchi K. Bacterial biomechanics-From individual behaviors to biofilm and the gut flora. APL Bioeng 2020; 4:041504. [PMID: 33163845 PMCID: PMC7595747 DOI: 10.1063/5.0026953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria inhabit a variety of locations and play important roles in the environment and health. Our understanding of bacterial biomechanics has improved markedly in the last decade and has revealed that biomechanics play a significant role in microbial biology. The obtained knowledge has enabled investigation of complex phenomena, such as biofilm formation and the dynamics of the gut flora. A bottom-up strategy, i.e., from the cellular to the macroscale, facilitates understanding of macroscopic bacterial phenomena. In this Review, we first cover the biomechanics of individual bacteria in the bulk liquid and on surfaces as the base of complex phenomena. The collective behaviors of bacteria in simple environments are next introduced. We then introduce recent advances in biofilm biomechanics, in which adhesion force and the flow environment play crucial roles. We also review transport phenomena in the intestine and the dynamics of the gut flora, focusing on that in zebrafish. Finally, we provide an overview of the future prospects for the field.
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Affiliation(s)
| | - Toshihiro Omori
- Department Finemechanics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
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Chu F, Esworthy RS, Shen B, Doroshow JH. Role of the microbiota in ileitis of a mouse model of inflammatory bowel disease-Glutathione peroxide isoenzymes 1 and 2-double knockout mice on a C57BL background. Microbiologyopen 2020; 9:e1107. [PMID: 32810389 PMCID: PMC7568258 DOI: 10.1002/mbo3.1107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/19/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022] Open
Abstract
C57Bl6 (B6) mice devoid of glutathione peroxidases 1 and 2 (Gpx1/2-DKO) develop ileitis after weaning. We previously showed germ-free Gpx1/2-DKO mice of mixed B6.129 background did not develop ileocolitis. Here, we examine the composition of the ileitis provoking microbiota in B6 Gpx1/2-DKO mice. DNA was isolated from the ileum fecal stream and subjected to high-throughput sequencing of the V3 and V4 regions of the 16S rRNA gene to determine the abundance of operational taxonomic units (OTUs). We analyzed the role of bacteria by comparing the microbiomes of the DKO and pathology-free non-DKO mice. Mice were treated with metronidazole, streptomycin, and vancomycin to alter pathology and correlate the OTU abundances with pathology levels. Principal component analysis based on Jaccard distance of abundance showed 3 distinct outcomes relative to the source Gpx1/2-DKO microbiome. Association analyses of pathology and abundance of OTUs served to rule out 7-11 of 24 OTUs for involvement in the ileitis. Collections of OTUs were identified that appeared to be linked to ileitis in this animal model and would be classified as commensals. In Gpx1/2-DKO mice, host oxidant generation from NOX1 and DUOX2 in response to commensals may compromise the ileum epithelial barrier, a role generally ascribed to oxidants generated from mitochondria, NOX2 and endoplasmic reticulum stress in response to presumptive pathogens in IBD. Elevated oxidant levels may contribute to epithelial cell shedding, which is strongly associated with progress toward inflammation in Gpx1/2-DKO mice and predictive of relapse in IBD by allowing leakage of microbial components into the submucosa.
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Affiliation(s)
- Fong‐Fong Chu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital and College of Clinical Medicine of HenanUniversity of Science and TechnologyLuoyangChina
| | - R. Steven Esworthy
- Department of Cancer Genetics and EpigeneticsBeckman Research InstituteCity of HopeDuarteCAUSA
| | - Binghui Shen
- Department of Cancer Genetics and EpigeneticsBeckman Research InstituteCity of HopeDuarteCAUSA
| | - James H. Doroshow
- Center for Cancer Research and Division of Cancer Treatment and DiagnosisNational Cancer InstituteBethesdaMDUSA
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Schmiedová L, Kreisinger J, Požgayová M, Honza M, Martin JF, Procházka P. Gut microbiota in a host-brood parasite system: insights from common cuckoos raised by two warbler species. FEMS Microbiol Ecol 2020; 96:5872480. [PMID: 32672792 DOI: 10.1093/femsec/fiaa143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/15/2020] [Indexed: 11/13/2022] Open
Abstract
An animal's gut microbiota (GM) is shaped by a range of environmental factors affecting the bacterial sources invading the host. At the same time, animal hosts are equipped with intrinsic mechanisms enabling regulation of GM. However, there is limited knowledge on the relative importance of these forces. To assess the significance of host-intrinsic vs environmental factors, we studied GM in nestlings of an obligate brood parasite, the common cuckoo (Cuculus canorus), raised by two foster species, great reed warblers (Acrocephalus arundinaceus) and Eurasian reed warblers (A. scirpaceus), and compared these with GM of the fosterers' own nestlings. We show that fecal GM varied between cuckoo and warbler nestlings when accounting for the effect of foster/parent species, highlighting the importance of host-intrinsic regulatory mechanisms. In addition to feces, cuckoos also expel a deterrent secretion, which provides protection against olfactory predators. We observed an increased abundance of bacterial genera capable of producing repulsive volatile molecules in the deterrent secretion. Consequently, our results support the hypothesis that microbiota play a role in this antipredator mechanism. Interestingly, fosterer/parent identity affected only cuckoo deterrent secretion and warbler feces microbiota, but not that of cuckoo feces, suggesting a strong selection of bacterial strains in the GM by cuckoo nestlings.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12800 Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12800 Prague, Czech Republic
| | - Milica Požgayová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, CZ-60365 Brno, Czech Republic
| | - Marcel Honza
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, CZ-60365 Brno, Czech Republic
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, CZ-60365 Brno, Czech Republic
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Yanni AE, Mitropoulou G, Prapa I, Agrogiannis G, Kostomitsopoulos N, Bezirtzoglou E, Kourkoutas Y, Karathanos VT. Functional modulation of gut microbiota in diabetic rats following dietary intervention with pistachio nuts ( Pistacia vera L.). Metabol Open 2020; 7:100040. [PMID: 32812934 PMCID: PMC7424811 DOI: 10.1016/j.metop.2020.100040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/01/2020] [Accepted: 06/13/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Gut microbiota holds a key-role in numerous biological functions and has emerged as a driving force for the development of diabetes. Diet contributes to gut microbiota diversity and functionality providing a tool for the prevention and management of the disease. The study aimed to investigate the effect of a dietary intervention with pistachio nuts, a rich source of monounsaturated fatty acids, dietary fibers and phytochemicals on gut microbiota composition in the rat model of Type 1 Diabetes. METHODS Male Wistar rats were randomly assigned into four groups: healthy animals which received control diet (CD) or pistachio diet (PD), and diabetic animals which received control diet (DCD) or pistachio diet (DPD) for 4 weeks. Plasma biochemical parameters were determined and histological examination of liver and pancreas was performed at the end of the dietary intervention. Adherent intestinal microbiota populations in jejunum, ileum, caecum and colon were analyzed. Fecal microbiota populations at the beginning and the end of the study were determined by microbiological analysis and 16S rRNA sequencing. RESULTS Diabetic animals of both groups exhibited high plasma glucose and low insulin concentrations, as well as characteristic pancreatic lesions. Pistachio supplementation significantly increased lactobacilli and bifidobacteria populations in jejunum, ileum and caecum (p < 0.05) and normalized microbial flora in all examined intestinal regions of diabetic animals. After 4 weeks of supplementation, populations of bifidobacteria and lactobacilli were increased in feces of both healthy and diabetic animals, while enterococci levels were decreased (p < 0.05). Next Generation Sequencing of fecal samples revealed increased and decreased counts of Firmicutes and Bacteroidetes, respectively, in healthy animals that received the pistachio diet. Actinobacteria OTUs were higher in diabetic animals and increased over time in the pistachio treated groups, along with increased abundance of Bifidobacterium. Lactobacillus, Turicibacter and Romboutsia populations were elevated in healthy animals administered the pistachio nuts. Of note, relative abundance of Bacteroides was higher in healthy than in diabetic rats (p < 0.05). CONCLUSION Dietary pistachio restored normal flora and enhanced the presence of beneficial microbes in the rat model of streptozotocin-induced diabetes.
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Affiliation(s)
- Amalia E. Yanni
- Laboratory of Chemistry, Biochemistry, Physical Chemistry of Foods, Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Gregoria Mitropoulou
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, GR, 68100, Greece
| | - Ioanna Prapa
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, GR, 68100, Greece
| | - Georgios Agrogiannis
- First Department of Pathology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Yiannis Kourkoutas
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, GR, 68100, Greece
| | - Vaios T. Karathanos
- Laboratory of Chemistry, Biochemistry, Physical Chemistry of Foods, Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
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Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study. Sci Rep 2020; 10:13246. [PMID: 32764739 PMCID: PMC7413396 DOI: 10.1038/s41598-020-70249-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
Animal-associated microbiota is expected to impose crucial effects on the host's fitness-related performance, including reproduction. Most research to date has focused on interactions between the host with its gut microbiota; however, there remain considerable gaps in knowledge regarding microbial consortia in other organs, including interspecific divergence, temporal stability, variation drivers, and their effects on the host. To fill these gaps, we examined oral and vaginal microbiota composition in four free-living mouse species of the genus Apodemus, each varying in the degree of female promiscuity. To assess temporal stability and microbiota resistance to environmental change, we exposed one of the species, Apodemus uralensis, to standardized captive conditions and analyzed longitudinal changes in its microbiota structure. Our results revealed the existence of a "core" oral microbiota that was not only shared among all four species but also persisted almost unchanged in captivity. On the other hand, vaginal microbiota appears to be more plastic in captive conditions and less species-specific in comparison with oral microbiota. This study is amongst the first to describe oral microbiota dynamics. Furthermore, the vaginal microbiota results are especially surprising in light of the well-known role of stable vaginal microbiota as a defense against pathogens. The results indicate the existence of diverse mechanisms that shape each microbiota. On the other hand, our data provides somewhat ambiguous support for the systematic effect of phylogeny and social system on both oral and vaginal microbiota structures.
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Bendová B, Piálek J, Ďureje Ľ, Schmiedová L, Čížková D, Martin JF, Kreisinger J. How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies. BMC Microbiol 2020; 20:194. [PMID: 32631223 PMCID: PMC7336484 DOI: 10.1186/s12866-020-01859-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition of free-living individuals can change dramatically. At present, little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Here, we compare the taxonomic composition and diversity of bacterial and fungal communities across three gut sections in synanthropic house mouse (Mus musculus) and a closely related non-synanthropic mound-building mouse (Mus spicilegus). Results Using Illumina sequencing of bacterial 16S rRNA amplicons, we found higher bacterial diversity in M. spicilegus and detected 11 bacterial operational taxonomic units with significantly different proportions. Notably, abundance of Oscillospira, which is typically higher in lean or outdoor pasturing animals, was more abundant in non-commensal M. spicilegus. ITS2-based barcoding revealed low diversity and high uniformity of gut fungi in both species, with the genus Kazachstania clearly dominant. Conclusions Though differences in gut bacteria observed in the two species can be associated with their close association with humans, changes due to a move from commensalism to captivity would appear to have caused larger shifts in microbiota.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Dagmar Čížková
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jean-Francois Martin
- CBGP, Montpellier SupAgro, INRA, CIRAD, IRD, Univ Montpellier, Montferrier-sur-Lez, France
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
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Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice. ISME JOURNAL 2020; 14:2367-2380. [PMID: 32518248 PMCID: PMC7490391 DOI: 10.1038/s41396-020-0690-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022]
Abstract
The house mouse is a key model organism in skin research including host–microbiota interactions, yet little is known about the skin microbiota of free-living mice. It is similarly unclear how closely laboratory mice, which typically live under exceptionally hygienic conditions, resemble the ancestral state of microbial variation in the wild. In this study, we sampled an area spanning 270 km2 in south-west France and collected 203 wild Mus musculus domesticus. We profiled the ear skin microbiota on standing and active communities (DNA-based and RNA-based 16 rRNA gene sequencing, respectively), and compared multiple community aspects between wild-caught and laboratory-reared mice kept in distinct facilities. Compared to lab mice, we reveal the skin microbiota of wild mice on the one hand to be unique in their composition within the Staphylococcus genus, with a majority of sequences most closely matching known novobiocin-resistant species, and display evidence of a rare biosphere. On the other hand, despite drastic disparities between natural and laboratory environments, we find that shared taxa nonetheless make up the majority of the core skin microbiota of both wild- and laboratory skin communities, suggesting that mammalian skin is a highly specialized habitat capable of strong selection from available species pools. Finally, the influence of environmental factors suggests RNA-based profiling as a preferred method to reduce environmental noise.
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Suzuki TA, Martins FM, Phifer-Rixey M, Nachman MW. The gut microbiota and Bergmann's rule in wild house mice. Mol Ecol 2020; 29:2300-2311. [PMID: 32419280 DOI: 10.1111/mec.15476] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 12/16/2022]
Abstract
The extent to which the gut microbiota may play a role in latitudinal clines of body mass variation (i.e., Bergmann's rule) remains largely unexplored. Here, we collected wild house mice from three latitudinal transects across North and South America and investigated the relationship between variation in the gut microbiota and host body mass by combining field observations and common garden experiments. First, we found that mice in the Americas follow Bergmann's rule, with increasing body mass at higher latitudes. Second, we found that overall differences in the gut microbiota were associated with variation in body mass controlling for the effects of latitude. Then, we identified specific microbial measurements that show repeated associations with body mass in both wild-caught and laboratory-reared mice. Finally, we found that mice from colder environments tend to produce greater amounts of bacteria-driven energy sources (i.e., short-chain fatty acids) without an increase in food consumption. Our findings provide motivation for future faecal transplant experiments directly testing the intriguing possibility that the gut microbiota may contribute to Bergmann's rule, a fundamental pattern in ecology.
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Affiliation(s)
- Taichi A Suzuki
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Felipe M Martins
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA.,Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA.,Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
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Corl A, Charter M, Rozman G, Toledo S, Turjeman S, Kamath PL, Getz WM, Nathan R, Bowie RCK. Movement ecology and sex are linked to barn owl microbial community composition. Mol Ecol 2020; 29:1358-1371. [PMID: 32115796 DOI: 10.1111/mec.15398] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/15/2020] [Accepted: 02/24/2020] [Indexed: 12/26/2022]
Abstract
The behavioural ecology of host species is likely to affect their microbial communities, because host sex, diet, physiology, and movement behaviour could all potentially influence their microbiota. We studied a wild population of barn owls (Tyto alba) and collected data on their microbiota, movement, diet, size, coloration, and reproduction. The composition of bacterial species differed by the sex of the host and female owls had more diverse bacterial communities than their male counterparts. The abundance of two families of bacteria, Actinomycetaceae and Lactobacillaceae, also varied between the sexes, potentially as a result of sex differences in hormones and immunological function, as has previously been found with Lactobacillaceae in the microbiota of mice. Male and female owls did not differ in the prey they brought to the nest, which suggests that dietary differences are unlikely to underlie the differences in their microbiota. The movement behaviour of the owls was associated with the host microbiota in both males and females because owls that moved further from their nest each day had more diverse bacterial communities than owls that stayed closer to their nests. This novel result suggests that the movement ecology of hosts can impact their microbiota, potentially on the basis of their differential encounters with new bacterial species as the hosts move and forage across the landscape. Overall, we found that many aspects of the microbial community are correlated with the behavioural ecology of the host and that data on the microbiota can aid in generating new hypotheses about host behaviour.
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Affiliation(s)
- Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Motti Charter
- Movement Ecology Laboratory, Department of Ecology, Evolution, and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Shamir Research Institute and Department of Geography and Environmental Studies, University of Haifa, Haifa, Israel
| | - Gabe Rozman
- Movement Ecology Laboratory, Department of Ecology, Evolution, and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Toledo
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Sondra Turjeman
- Movement Ecology Laboratory, Department of Ecology, Evolution, and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Wayne M Getz
- Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.,School of Mathematical Sciences, University of KwaZulu, Natal, South Africa
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution, and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
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Bogatyrev SR, Rolando JC, Ismagilov RF. Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine. MICROBIOME 2020; 8:19. [PMID: 32051033 PMCID: PMC7017497 DOI: 10.1186/s40168-020-0785-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/05/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract. RESULTS In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine. CONCLUSIONS Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis. Video abstract.
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Affiliation(s)
- Said R Bogatyrev
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Justin C Rolando
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, USA.
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Han X, Shao H, Wang Y, Hu A, Chen R, Chen Q. Composition of the bacterial community in the gastrointestinal tract of Kunming mice. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2019.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Chu FF, Esworthy RS, Shen B, Gao Q, Doroshow JH. Dexamethasone and Tofacitinib suppress NADPH oxidase expression and alleviate very-early-onset ileocolitis in mice deficient in GSH peroxidase 1 and 2. Life Sci 2019; 239:116884. [PMID: 31689440 PMCID: PMC6898790 DOI: 10.1016/j.lfs.2019.116884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/25/2022]
Abstract
C57BL6/J (B6) mice lacking Se-dependent GSH peroxidase 1 and 2 (GPx1/2-DKO) develop mild to moderate ileocolitis around weaning. These DKO mice have a disease resembling human very-early-onset inflammatory bowel disease (VEOIBD), which is associated with mutations in NADPH oxidase genes. Drugs including dexamethasone (Dex), Tofacitinib (Tofa; a Janus kinase/JAK inhibitor) and anti-TNF antibody are effective to treat adult, but not pediatric IBD. AIMS To test the efficacy of hydrophobic Dex and hydrophilic Dex phosphate (Dex phos), Tofa, anti-Tnf Ab, Noxa1ds-TAT and gp91ds-TAT peptides (inhibiting NOX1 and NOX2 assembly respectively), antioxidant MJ33 and ML090, and pifithrin-α (p53 inhibitor) on alleviation of gut inflammation in DKO weanlings. MAIN METHODS All treatments began on 22-day-old GPx1/2-DKO mice. The mouse intestine pathology was compared between the drug- and vehicle-treated groups after six or thirteen days of treatment. KEY FINDINGS Among all drugs tested, Dex, Dex phos and Tofa were the strongest to suppress ileocolitis in the DKO weanlings. Dex, Dex phos and Tofa inhibited crypt apoptosis and increased crypt density. Dex or Dex phos alone also inhibited cell proliferation, exfoliation and crypt abscess in the ileum. Dex, but not Tofa, retarded mouse growth. Both Dex and Tofa inhibited ileum Nox1, Nox4 and Duox2, but not Nox2 gene expression. Noxa1ds-TAT and gp91ds-TAT peptides as well as MJ33 had subtle effect on suppressing pathology, while others had negligible effect. SIGNIFICANCE These findings suggest that NADPH oxidases can be novel drug targets for pediatric IBD therapy, and Tofa may be considered for treating VEOIBD.
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Affiliation(s)
- Fong-Fong Chu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan, 471003, China; Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA.
| | - R Steven Esworthy
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA.
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA.
| | - Qiang Gao
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan, 471003, China; Department of Gastroenterology and Hepatology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, 100144, China.
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, NIH, Bethesda, MD, USA.
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Reed A, Pigage JC, Pigage HK, Glickman C, Bono JM. Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species ( Sciurus aberti and S. niger) living in sympatry. Ecol Evol 2019; 9:13344-13358. [PMID: 31871649 PMCID: PMC6912893 DOI: 10.1002/ece3.5789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro-organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber-rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.
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Affiliation(s)
- Andrew Reed
- Biology DepartmentUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
| | - Jon C. Pigage
- Biology DepartmentUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
| | - Helen K. Pigage
- Biology DepartmentUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
| | - Cody Glickman
- Computational Bioscience Graduate ProgramUniversity of Colorado Denver Anschutz Medical CampusAuroraCOUSA
| | - Jeremy M. Bono
- Biology DepartmentUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
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43
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Nadatani Y, Watanabe T, Suda W, Nakata A, Matsumoto Y, Kosaka S, Higashimori A, Otani K, Hosomi S, Tanaka F, Nagami Y, Kamata N, Taira K, Yamagami H, Tanigawa T, Hattori M, Fujiwara Y. Gastric acid inhibitor aggravates indomethacin-induced small intestinal injury via reducing Lactobacillus johnsonii. Sci Rep 2019; 9:17490. [PMID: 31767915 PMCID: PMC6877529 DOI: 10.1038/s41598-019-53559-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Proton pump inhibitors (PPIs) alter the composition of the intestinal microbiome, exacerbating indomethacin (IND)-induced small intestinal damage. Vonoprazan fumarate inhibits gastric acid secretion using a different mechanism from PPIs. We investigated the effects of both drugs on the intestinal microbiome and IND-induced small intestinal damage. We sought to clarify whether PPI-induced dysbiosis and worsening of the damage were due to a specific drug class effect of PPIs. Rabeprazole administration increased operational taxonomic unit numbers in the small intestines of C57BL/6 J mice, whereas the difference was not significant in the vonoprazan-treated group but exhibited a trend. Permutational multivariate analysis of variance of the unweighted UniFrac distances showed significant differences between vehicle- and vonoprazan- or rabeprazole-treated groups. L. johnsonii was the predominant microbial species, and the population ratio decreased after vonoprazan and rabeprazole administration. The vonoprazan- and rabeprazole-treated groups showed increased IND-induced damage. This high sensitivity to IND-induced damage was evaluated by transplantation with contents from the small intestine of mice treated with either vonoprazan or rabeprazole. Supplementation of L. johnsonii orally in mice treated with rabeprazole and vonoprazan prevented the increase in IND-induced small intestinal damage. In conclusion, both rabeprazole and vonoprazan aggravated NSAID-induced small intestinal injury by reducing the population of L. johnsonii in the small intestine via suppressing gastric acid secretion.
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Affiliation(s)
- Yuji Nadatani
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Toshio Watanabe
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan.
| | - Wataru Suda
- Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Akinobu Nakata
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yuji Matsumoto
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Satoshi Kosaka
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Akira Higashimori
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Koji Otani
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Shuhei Hosomi
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Fumio Tanaka
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yasuaki Nagami
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Noriko Kamata
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Koichi Taira
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hirokazu Yamagami
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Tetsuya Tanigawa
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan.,Graduat Graduate e School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yasuhiro Fujiwara
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
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44
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Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis. PLoS One 2019; 14:e0225079. [PMID: 31703107 PMCID: PMC6839838 DOI: 10.1371/journal.pone.0225079] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022] Open
Abstract
Crohn’s Disease and Ulcerative Colitis are chronic, inflammatory conditions of the digestive tract, collectively known as Inflammatory Bowel Disease (IBD). The combined influence of lifestyle factors, genetics, and the gut microbiome contribute to IBD pathogenesis. Studies of the gut microbiome have shown significant differences in its composition between healthy individuals and those with IBD. Due to the high inter-individual microbiome variation seen in humans, mouse models of IBD are often used to investigate potential IBD mechanisms and their interplay between host, microbial, and environmental factors. While fecal samples are the predominant material used for microbial community analysis, they may not be the ideal sample to use for analysis of the microbiome of mice with experimental colitis, such as that induced by 2, 4, 6 trinitrobenzesulfonic acid (TNBS). As TNBS is administered intrarectally to induce colitis and inflammation is confined to the colon in this model, we hypothesized that the microbiome of the colonic mucus would most closely correlate with TNBS colitis severity. Based on our previous research, we also hypothesized that sex would be associated with both disease severity and microbial differences in mice with chronic TNBS colitis. We examined and compared the fecal, cecal content, and colonic mucus microbiota of 8-week old male and female C57BL/6J wild-type mice prior to and after the induction of TNBS colitis via 16S rRNA gene sequencing. We found that the colonic mucus microbiome was more closely correlated with disease severity than were alterations in the fecal and cecal microbiomes. We also found that the microbiomes of the feces, cecum, and mucus were distinct, but found no significant differences that were associated with sex in either compartment. Our findings highlight the importance of sampling colonic mucus in TNBS-induced colitis. Moreover, consideration of the differential impact of sex on the microbiome across mouse strains may be critical for the appropriate application of TNBS colitis models and robust comparisons across studies in the future.
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45
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Warren MF, Hallowell HA, Higgins KV, Liles MR, Hood WR. Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat ( Rattus norvegicus) Model. Nutrients 2019; 11:E2257. [PMID: 31546967 PMCID: PMC6769776 DOI: 10.3390/nu11092257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 12/23/2022] Open
Abstract
Historically, investigators have assumed microorganisms identified in mother's milk to be contaminants, but recent data suggest that milk microbiota may contribute to beneficial maternal effects. Microorganisms that colonize the gastrointestinal tracts of newborn mammals are derived, at least in part, from the maternal microbial population. Milk-derived microbiota is an important source of this microbial inocula and we hypothesized that the maternal diet contributes to variation in this microbial community. To evaluate the relationship between a mother's diet and milk microbiome, we fed female rats a low- or high-protein diet and mated all individuals. Milk and cecal contents were collected from dams at peak lactation (14-day post-partum), and the bacterial composition of each community was assessed by 16S rRNA gene amplicon sequencing. Our findings revealed higher dietary protein intake decreased fecal microbial diversity but increased milk microbial and pup cecum diversity. Further, the higher dietary protein intake resulted in a greater abundance of potentially health-promoting bacteria, such as Lactobacillus spp. These data suggest that dietary protein levels contribute to significant shifts in the composition of maternal milk microbiota and that the functional consequences of these changes in microbial inocula might be biologically important and should be further explored.
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Affiliation(s)
- Matthew F Warren
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA.
| | - Haley A Hallowell
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Keah V Higgins
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
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46
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Yan W, Sun C, Zheng J, Wen C, Ji C, Zhang D, Chen Y, Hou Z, Yang N. Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota. Front Microbiol 2019; 10:2126. [PMID: 31572332 PMCID: PMC6753641 DOI: 10.3389/fmicb.2019.02126] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11-87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54-0.71 and 0.71-0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = -0.2-0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.
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Affiliation(s)
- Wei Yan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congliang Ji
- Wen’s sNanfang Poultry Breeding Co. Ltd., Yunfu, China
| | - Dexiang Zhang
- Wen’s sNanfang Poultry Breeding Co. Ltd., Yunfu, China
| | - Yonghua Chen
- Wen’s sNanfang Poultry Breeding Co. Ltd., Yunfu, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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47
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Lin M, Zeng C, Li Z, Ma Y, Jia X. Comparative analysis of the composition and function of fecal-gut bacteria in captive juvenile Crocodylus siamensis between healthy and anorexic individuals. Microbiologyopen 2019; 8:e929. [PMID: 31482690 PMCID: PMC6925159 DOI: 10.1002/mbo3.929] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/05/2023] Open
Abstract
The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential role in host physiological activity, and it contributes significantly to both the health and diseased states of animals. However, thus far, no study has focused on the correlation between diseases and intestinal bacterial communities in crocodilians. Here, we first compared the composition and function of gut microbial communities in captive juvenile C. siamensis suffering from anorexia and healthy crocodile controls using deep amplicon sequencing. The gut microbial diversity of anorexic crocodiles was much lower than the healthy individuals. Obvious changes in gut microbial composition were observed between sick and healthy crocodiles, except for Cetobacterium somerae of phylum Fusobacteria. In particular, the abundance of Bacteroides luti, Clostridium disporicum, Plesiomonas shigelloides, and Odoribacter sp. in the gut flora of healthy crocodiles was distinctly higher than the diseased group. Conversely, the species Edwardsiella tarda was overrepresented in the gut of anorexic crocodiles compared to the healthy group. Furthermore, in anorexic crocodiles, the predicted microbial functions that were related to amino acid metabolism, biosynthesis of other secondary metabolites, nucleotide metabolism, replication and repair, and translation were significantly reduced, while signal transduction was significantly enriched. These findings of the present study provide a reference to enrich the field of gut microorganism studies in crocodilians and suggest that alterations in the composition and function of gut bacteria in C. siamensis juveniles may be associated with anorexia in crocodiles.
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Affiliation(s)
- Mao Lin
- Engineering-Technology Research Center for Fishery Medicine, Fisheries College, Jimei University, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Chenxi Zeng
- Engineering-Technology Research Center for Fishery Medicine, Fisheries College, Jimei University, Xiamen, China
| | - Zhongqin Li
- Engineering-Technology Research Center for Fishery Medicine, Fisheries College, Jimei University, Xiamen, China
| | - Ying Ma
- Engineering-Technology Research Center for Fishery Medicine, Fisheries College, Jimei University, Xiamen, China
| | - Xueqing Jia
- Engineering-Technology Research Center for Fishery Medicine, Fisheries College, Jimei University, Xiamen, China
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48
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Abstract
The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota. The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus. Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species. IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.
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49
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Tang W, Zhu G, Shi Q, Yang S, Ma T, Mishra SK, Wen A, Xu H, Wang Q, Jiang Y, Wu J, Xie M, Yao Y, Li D. Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions. Microbiologyopen 2019; 8:e00789. [PMID: 30848054 PMCID: PMC6612554 DOI: 10.1002/mbo3.789] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
The gut microbiota helps the host to absorb nutrients and generate immune responses that can affect host behavior, development, reproduction, and overall health. However, in most of the previous studies, microbiota was sampled mainly using feces and intestinal contents from mammals but not from wild reptiles. Here, we described the bacterial profile from five different gastrointestinal tract (GIT) segments (esophagus, stomach, small intestine, large intestine, and cloaca) of three wild Rhabdophis subminiatus using 16S rRNA V4 hypervariable amplicon sequencing. Forty-seven bacterial phyla were found in the entire GIT, of which Proteobacteria, Firmicutes, and Bacteroidetes were predominant. The results showed a significant difference in microbial diversity between the upper GIT segments (esophagus and stomach) and lower GIT segments (large intestine and cloaca). An obvious dynamic distribution of Fusobacteria and Bacteroidetes was observed, which mainly existed in the lower GIT segments. Conversely, the distribution of Tenericutes was mainly observed in the upper GIT. We also predicted the microbial functions in the different GIT segments, which showed that microbiota in each segments played an important role in higher membrane transport and carbohydrate and amino acid metabolism. Microbes in the small intestine were also mainly involved in disease-related systems, while in the large intestine, they were associated with membrane transport and carbohydrate metabolism. This is the first study to investigate the distribution of the gut microbiota and to predict the microbial function in R. subminiatus. The composition of the gut microbiota certainly reflects the diet and the living environment of the host. Furthermore, these findings provide vital evidence for the diagnosis and treatment of gut diseases in snakes and offer a direction for a model of energy budget research.
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Affiliation(s)
- Wenjiao Tang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Guangxiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qian Shi
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Shijun Yang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Shailendra Kumar Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Anxiang Wen
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Huailiang Xu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qin Wang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yanzhi Jiang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Jiayun Wu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Meng Xie
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yongfang Yao
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
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50
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Suzuki TA, Phifer-Rixey M, Mack KL, Sheehan MJ, Lin D, Bi K, Nachman MW. Host genetic determinants of the gut microbiota of wild mice. Mol Ecol 2019; 28:3197-3207. [PMID: 31141224 DOI: 10.1111/mec.15139] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/26/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
Abstract
Identifying a common set of genes that mediate host-microbial interactions across populations and species of mammals has broad relevance for human health and animal biology. However, the genetic basis of the gut microbial composition in natural populations remains largely unknown outside of humans. Here, we used wild house mouse populations as a model system to ask three major questions: (a) Does host genetic relatedness explain interindividual variation in gut microbial composition? (b) Do population differences in the microbiota persist in a common environment? (c) What are the host genes associated with microbial richness and the relative abundance of bacterial genera? We found that host genetic distance is a strong predictor of the gut microbial composition as characterized by 16S amplicon sequencing. Using a common garden approach, we then identified differences in microbial composition between populations that persisted in a shared laboratory environment. Finally, we used exome sequencing to associate host genetic variants with microbial diversity and relative abundance of microbial taxa in wild mice. We identified 20 genes that were associated with microbial diversity or abundance including a macrophage-derived cytokine (IL12a) that contained three nonsynonymous mutations. Surprisingly, we found a significant overrepresentation of candidate genes that were previously associated with microbial measurements in humans. The homologous genes that overlapped between wild mice and humans included genes that have been associated with traits related to host immunity and obesity in humans. Gene-bacteria associations identified in both humans and wild mice suggest some commonality to the host genetic determinants of gut microbial composition across mammals.
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Affiliation(s)
- Taichi A Suzuki
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Megan Phifer-Rixey
- Department of Biology, Monmouth University, West Long Branch, New Jersey, USA
| | - Katya L Mack
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Dana Lin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Ke Bi
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, USA
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
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