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Shao W, Pan B, Li Z, Peng R, Yang W, Xie Y, Han D, Fang X, Li J, Zhu Y, Zhao Z, Kan H, Ying Z, Xu Y. Gut microbiota mediates ambient PM 2.5 exposure-induced abnormal glucose metabolism via short-chain fatty acids. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135096. [PMID: 38996677 DOI: 10.1016/j.jhazmat.2024.135096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
PM2.5 exposure has been found to cause gut dysbiosis and impair glucose homeostasis in human and animals, yet their underlying biological connection remain unclear. In the present study, we aim to investigate the biological significance of gut microbiota in PM2.5-induced glucose metabolic abnormalities. Our results showed that microbiota depletion by antibiotics treatment significantly alleviated PM2.5-induced glucose intolerance and insulin resistance, as indicated by the intraperitoneal glucose tolerance test, glucose-induced insulin secretion, insulin tolerance test, insulin-induced phosphorylation levels of Akt and GSK-3β in insulin sensitive tissues. In addition, faecal microbiota transplantation (FMT) from PM2.5-exposed donor mice successfully remodeled the glucose metabolism abnormalities in recipient mice, while the transplantation of autoclaved faecal materials did not. Faecal microbiota analysis demonstrated that the composition and alpha diversity of the gut bacterial community were altered by PM2.5 exposure and in FMT recipient mice. Furthermore, short-chain fatty acids levels analysis showed that the circulating acetate was significantly decreased in PM2.5-exposed donor and FMT recipient mice, and supplementation of sodium acetate for 3 months successfully improved the glucose metabolism abnormalities induced by PM2.5 exposure. These results indicate that manipulating gut microbiota or its metabolites could be a potential strategy for preventing the adverse health effects of ambient PM2.5.
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Affiliation(s)
- Wenpu Shao
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Bin Pan
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Zhouzhou Li
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Renzhen Peng
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Wenhui Yang
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Yuanting Xie
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Dongyang Han
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Xinyi Fang
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Jingyu Li
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Yaning Zhu
- Department of Pathology, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, Huaian, China.
| | - Zhuohui Zhao
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Haidong Kan
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
| | - Zhekang Ying
- Department of Medicine Cardiology Division, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Yanyi Xu
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment, Fudan University, Shanghai, China.
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2
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Auclert LZ, Chhanda MS, Derome N. Interwoven processes in fish development: microbial community succession and immune maturation. PeerJ 2024; 12:e17051. [PMID: 38560465 PMCID: PMC10981415 DOI: 10.7717/peerj.17051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.
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Affiliation(s)
- Lisa Zoé Auclert
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Mousumi Sarker Chhanda
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Basherhat, Bangladesh
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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3
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de Wit DF, Hanssen NMJ, Wortelboer K, Herrema H, Rampanelli E, Nieuwdorp M. Evidence for the contribution of the gut microbiome to obesity and its reversal. Sci Transl Med 2023; 15:eadg2773. [PMID: 37992156 DOI: 10.1126/scitranslmed.adg2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/27/2023] [Indexed: 11/24/2023]
Abstract
Obesity has become a worldwide pandemic affecting more than 650 million people and is associated with a high burden of morbidity. Alongside traditional risk factors for obesity, the gut microbiome has been identified as a potential factor in weight regulation. Although rodent studies suggest a link between the gut microbiome and body weight, human evidence for causality remains scarce. In this Review, we postulate that existing evidence remains to establish a contribution of the gut microbiome to the development of obesity in humans but that modified probiotic strains and supraphysiological dosages of microbial metabolites may be beneficial in combatting obesity.
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Affiliation(s)
- Douwe F de Wit
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
| | - Nordin M J Hanssen
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
| | - Koen Wortelboer
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
| | - Hilde Herrema
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105AZ Amsterdam, Netherlands
| | - Elena Rampanelli
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Max Nieuwdorp
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
- Amsterdam UMC location Vrije Universiteit Medical Center, Department of Internal Medicine, Diabetes Center, 1105AZ Amsterdam, Netherlands
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4
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Xue KS, Walton SJ, Goldman DA, Morrison ML, Verster AJ, Parrott AB, Yu FB, Neff NF, Rosenberg NA, Ross BD, Petrov DA, Huang KC, Good BH, Relman DA. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559480. [PMID: 37808827 PMCID: PMC10557656 DOI: 10.1101/2023.09.26.559480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
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Affiliation(s)
- Katherine S Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophie Jean Walton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Biophysics Training Program, Stanford, CA 94305, USA
| | - Doran A Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | | | | | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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5
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Gok Yavuz B, Datar S, Chamseddine S, Mohamed YI, LaPelusa M, Lee SS, Hu ZI, Koay EJ, Tran Cao HS, Jalal PK, Daniel-MacDougall C, Hassan M, Duda DG, Amin HM, Kaseb AO. The Gut Microbiome as a Biomarker and Therapeutic Target in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:4875. [PMID: 37835569 PMCID: PMC10571776 DOI: 10.3390/cancers15194875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
The microbiome is pivotal in maintaining health and influencing disease by modulating essential inflammatory and immune responses. Hepatocellular carcinoma (HCC), ranking as the third most common cause of cancer-related fatalities globally, is influenced by the gut microbiome through bidirectional interactions between the gut and liver, as evidenced in both mouse models and human studies. Consequently, biomarkers based on gut microbiota represent promising non-invasive tools for the early detection of HCC. There is a growing body of evidence suggesting that the composition of the gut microbiota may play a role in the efficacy of immunotherapy in different types of cancer; thus, it could be used as a predictive biomarker. In this review, we will dissect the gut microbiome's role as a potential predictive and diagnostic marker in HCC and evaluate the latest progress in leveraging the gut microbiome as a novel therapeutic avenue for HCC patients, with a special emphasis on immunotherapy.
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Affiliation(s)
- Betul Gok Yavuz
- Department of Medicine, University of Missouri, St. Louis, MO 63121, USA;
| | - Saumil Datar
- Department of Medicine, University of Texas at Houston, Houston, TX 77030, USA;
| | - Shadi Chamseddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.C.); (Y.I.M.); (S.S.L.); (Z.I.H.)
| | - Yehia I. Mohamed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.C.); (Y.I.M.); (S.S.L.); (Z.I.H.)
| | - Michael LaPelusa
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Sunyoung S. Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.C.); (Y.I.M.); (S.S.L.); (Z.I.H.)
| | - Zishuo Ian Hu
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.C.); (Y.I.M.); (S.S.L.); (Z.I.H.)
| | - Eugene J. Koay
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Hop S. Tran Cao
- Hepato-Pancreato-Biliary Section, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Prasun Kumar Jalal
- Division of Gastroenterology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Carrie Daniel-MacDougall
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.D.-M.); (M.H.)
| | - Manal Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.D.-M.); (M.H.)
| | - Dan G. Duda
- Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA;
| | - Hesham M. Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Ahmed O. Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.C.); (Y.I.M.); (S.S.L.); (Z.I.H.)
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6
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Axenic and gnotobiotic insect technologies in research on host-microbiota interactions. Trends Microbiol 2023:S0966-842X(23)00055-0. [PMID: 36906503 DOI: 10.1016/j.tim.2023.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
Insects are one of the most important animal life forms on earth. Symbiotic microbes are closely related to the growth and development of the host insects and can affect pathogen transmission. For decades, various axenic insect-rearing systems have been developed, allowing further manipulation of symbiotic microbiota composition. Here we review the historical development of axenic rearing systems and the latest progress in using axenic and gnotobiotic approaches to study insect-microbe interactions. We also discuss the challenges of these emerging technologies, possible solutions to address these challenges, and future research directions that can contribute to a more comprehensive understanding of insect-microbe interactions.
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7
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Zhang W, Xie J, Xia S, Fan X, Schmitz-Esser S, Zeng B, Zheng L, Huang H, Wang H, Zhong J, Zhang Z, Zhang L, Jiang M, Hou R. Evaluating a potential model to analyze the function of the gut microbiota of the giant panda. Front Microbiol 2022; 13:1086058. [PMID: 36605506 PMCID: PMC9808404 DOI: 10.3389/fmicb.2022.1086058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
To contribute to the conservation of endangered animals, the utilization of model systems is critical to analyze the function of their gut microbiota. In this study, the results of a fecal microbial transplantation (FMT) experiment with germ-free (GF) mice receiving giant panda or horse fecal microbiota showed a clear clustering by donor microbial communities in GF mice, which was consistent with the results of blood metabolites from these mice. At the genus level, FMT re-established approximately 9% of the giant panda donor microbiota in GF mice compared to about 32% for the horse donor microbiota. In line with this, the difference between the panda donor microbiota and panda-mice microbiota on whole-community level was significantly larger than that between the horse donor microbiota and the horse-mice microbiota. These results were consistent with source tracking analysis that found a significantly higher retention rate of the horse donor microbiota (30.9%) than the giant panda donor microbiota (4.0%) in GF mice where the microbiota remained stable after FMT. Further analyzes indicated that the possible reason for the low retention rate of the panda donor microbiota in GF mice was a low relative abundance of Clostridiaceae in the panda donor microbiota. Our results indicate that the donor microbiota has a large effect on GF mice microbiota after FMT.
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Affiliation(s)
- Wenping Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China,*Correspondence: Wenping Zhang, ; Mingfeng Jiang, ; Rong Hou,
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China,Qinghai-Tibet Plateau Research Institute, Southwest Minzu University, Chengdu, Sichuan, China
| | - Shan Xia
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, Sichuan, China
| | - Xueyang Fan
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China
| | | | - Benhua Zeng
- Department of Infectious Diseases, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lijun Zheng
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China
| | - Jincheng Zhong
- Qinghai-Tibet Plateau Research Institute, Southwest Minzu University, Chengdu, Sichuan, China
| | - Zhihe Zhang
- Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China
| | - Mingfeng Jiang
- Qinghai-Tibet Plateau Research Institute, Southwest Minzu University, Chengdu, Sichuan, China,*Correspondence: Wenping Zhang, ; Mingfeng Jiang, ; Rong Hou,
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China,*Correspondence: Wenping Zhang, ; Mingfeng Jiang, ; Rong Hou,
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8
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Gan B, Sun N, Lai J, Wan Z, Li L, Wang Y, Zeng Y, Zeng D, Pan K, Fang J, Shu G, Wang H, Xin J, Ni X. Dynamic Monitoring of Changes in Fecal Flora of Giant Pandas in Mice: Co-Occurrence Network Reconstruction. Microbiol Spectr 2022; 11:e0199122. [PMID: 36472469 PMCID: PMC10100740 DOI: 10.1128/spectrum.01991-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Giant pandas are uniquely vulnerable mammals in western China. It is important to develop an animal model to explore the intestinal flora of giant pandas to understand the relationship between digestive diseases and flora. Existing animal models of intestinal flora focus on human flora-associated animals, such as mice, and there is a very limited amount of knowledge regarding giant panda flora-associated animals. To fill this gap, fecal microorganisms from giant pandas were transplanted into pseudosterile and germfree mice using single and multiple gavages. Fecal samples were collected from mice at four time points after transplantation for microbial community analysis. We determined that compared to pseudosterile mice, the characteristics of intestinal flora in pandas were better reproduced in germfree mice. There was no significant difference in microbial diversity between germfree mice and giant panda gut microbes from day 3 to day 21. Germfree mice at the phylum level possessed large amounts of Firmicutes and Proteobacteria, and at the genus level, Escherichia-Shigella, Clostridium sensu stricto 1, and Streptococcus dominated the intestinal flora structure. The microbial community co-occurrence network based on indicator species indicated that germfree mice transplanted with fecal bacteria tended to form a microbial community co-occurrence network similar to that of giant pandas, while pseudosterile mice tended to restore the microbial community co-occurrence network originally present in these mice. Our data are helpful for the study of giant panda flora-associated animals and provide new insights for the in vitro study of giant panda intestinal flora. IMPORTANCE The giant panda is a unique vulnerable mammal in western China, and its main cause of death is digestive system diseases regardless of whether these animals are in the wild or in captivity. The relationship between the intestinal flora and the host exerts a significant impact on the nutrition and health of the giant pandas. However, the protected status of the giant panda has made in vivo, repeatable, and large-sample sampling studies of their intestinal flora difficult. This greatly hinders the research depth of the giant panda intestinal flora from the source. The development and utilization of specific animal models to simulate the structure and characteristics of the intestinal flora provide another means to deal with these research limitations. However, current research examining giant panda flora-associated animals is limited. This study is the first to reveal dynamic changes in the fecal flora of giant pandas in mice after transplantation.
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Affiliation(s)
- Baoxing Gan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ning Sun
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Lai
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhiqiang Wan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lianxin Li
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanyan Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Fang
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Gang Shu
- Department of Pharmacy, College of Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hesong Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinge Xin
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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9
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Fernandes MR, Aggarwal P, Costa RGF, Cole AM, Trinchieri G. Targeting the gut microbiota for cancer therapy. Nat Rev Cancer 2022; 22:703-722. [PMID: 36253536 DOI: 10.1038/s41568-022-00513-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence suggests that the gut microbiota modulates the efficacy and toxicity of cancer therapy, most notably immunotherapy and its immune-related adverse effects. The poor response to immunotherapy in patients treated with antibiotics supports this influential role of the microbiota. Until recently, results pertaining to the identification of the microbial species responsible for these effects were incongruent, and relatively few studies analysed the underlying mechanisms. A better understanding of the taxonomy of the species involved and of the mechanisms of action has since been achieved. Defined bacterial species have been shown to promote an improved response to immune-checkpoint inhibitors by producing different products or metabolites. However, a suppressive effect of Gram-negative bacteria may be dominant in some unresponsive patients. Machine learning approaches trained on the microbiota composition of patients can predict the ability of patients to respond to immunotherapy with some accuracy. Thus, interest in modulating the microbiota composition to improve patient responsiveness to therapy has been mounting. Clinical proof-of-concept studies have demonstrated that faecal microbiota transplantation or dietary interventions might be utilized clinically to improve the success rate of immunotherapy in patients with cancer. Here, we review recent advances and discuss emerging strategies for microbiota-based cancer therapies.
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Affiliation(s)
- Miriam R Fernandes
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Poonam Aggarwal
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raquel G F Costa
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Alicia M Cole
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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10
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Chen X, Yan F, Liu T, Zhang Y, Li X, Wang M, Zhang C, Xu X, Deng L, Yao J, Wu S. Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant. Microbiol Spectr 2022; 10:e0044622. [PMID: 35924933 PMCID: PMC9430676 DOI: 10.1128/spectrum.00446-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/17/2022] [Indexed: 12/20/2022] Open
Abstract
The rumen, which contains a series of prokaryotes and eukaryotes with high abundance, determines the high ability to degrade complex carbohydrates in ruminants. Using 16S rRNA gene sequencing, we compared the ruminal microbiota of dairy goats with that in the foregut and colon of mice and found more Bacteroides identified in the rumen, which helps ruminants to utilize plant-derived polysaccharides, cellulose, and other structural carbohydrates. Furthermore, high-fiber diets did not significantly increase intestinal fiber-degrading bacteria in mice, but did produce higher levels of ruminal fiber-degrading bacteria in dairy goats. Through rumen microbe transplantation (RMT), we found that rumen-derived fiber-degrading bacteria can colonize the intestines of mice to exert their fiber-degrading function, but their colonization efficiency is affected by diet. Additionally, the colonization of these fiber-degrading bacteria in the colon may involve higher content of butyrate in the colon, protecting the colonic epithelial barrier and promoting energy metabolism. Overall, the fiber degradation function of rumen bacteria through RMT was verified, and our results provide new insights into isolating the functional and beneficial fiber-degrading bacteria in the rumen, providing a theoretical basis for the role of dietary fiber in intestinal health. IMPORTANCE Ruminants have a powerful progastric digestive system that converts structural carbohydrates into nutrients useful to humans. It is well known that this phenomenon is due to the fact that the rumen of ruminants is a natural microbial fermenter, which can ferment structural carbohydrates such as cellulose and hemicellulose and transform them into volatile fatty acids to supply energy for host. However, monogastric animals have an inherent disadvantage in utilizing fiber, so screening rumen-derived fiber-degrading bacteria as a fermentation strain for biological feed is needed in an attempt at improving the fiber digestibility of monogastric animals. In this study, a ruminal microbiota transplant experiment from goats to mice proves that ruminal microbiota could serve as a key factor in utilization of high-fiber diets and provides a new perspective for the development of probiotics with fiber degradation function from the rumen and the importance of the use of prebiotics during the intake of probiotics.
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Affiliation(s)
- Xiaodong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fang Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanling Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Mengya Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiurong Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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11
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Zhang T, Xiong J, Tian R, Li Y, Zhang Q, Li K, Xu X, Liang L, Zheng Y, Tian B. Effects of single- and mixed-bacterial inoculation on the colonization and assembly of endophytic communities in plant roots. FRONTIERS IN PLANT SCIENCE 2022; 13:928367. [PMID: 36105708 PMCID: PMC9464981 DOI: 10.3389/fpls.2022.928367] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/28/2022] [Indexed: 06/10/2023]
Abstract
The introduction and inoculation of beneficial bacteria in plants have consistently been considered as one of the most important ways to improve plant health and production. However, the effects of bacterial inoculation on the community assembly and composition of the root endophytic microbiome remain largely unknown. In this study, 55 strains were randomly isolated from tomato roots and then inoculated into wheat seeds singly or in combination. Most of the isolated bacterial strains showed an ability to produce lignocellulose-decomposing enzymes and promote plant growth. The results demonstrated that bacterial inoculation had a significant effect on the wheat root endophytic microbiome. The wheat root samples inoculated with single-bacterial species were significantly separated into two groups (A and B) that had different community structures and compositions. Among these, root endophytic communities for most wheat samples inoculated with a single-bacterial strain (Group A) were predominated by one or several bacterial species, mainly belonging to Enterobacterales. In contrast, only a few of the root samples inoculated with a single-bacterial strain (Group B) harbored a rich bacterial flora with relatively high bacterial diversity. However, wheat roots inoculated with a mixed bacterial complex were colonized by a more diverse and abundant bacterial flora, which was mainly composed of Enterobacterales, Actinomycetales, Bacillales, Pseudomonadales, and Rhizobiales. The results demonstrated that inoculation with bacterial complexes could help plants establish more balanced and beneficial endophytic communities. In most cases, bacterial inoculation does not result in successful colonization by the target bacterium in wheat roots. However, bacterial inoculation consistently had a significant effect on the root microbiome in plants. CAP analysis demonstrated that the variation in wheat root endophytic communities was significantly related to the taxonomic status and lignocellulose decomposition ability of the inoculated bacterial strain (p < 0.05). To reveal the role of lignocellulose degradation in shaping the root endophytic microbiome in wheat, four bacterial strains with different colonization abilities were selected for further transcriptome sequencing analysis. The results showed that, compared with that in the dominant bacterial species Ent_181 and Ent_189 of Group A, the expression of lignocellulose-decomposing enzymes was significantly downregulated in Bac_133 and Bac_71 (p < 0.05). In addition, we found that the dominant bacterial species of the tomato endophytic microbiome were more likely to become dominant populations in the wheat root microbiome. In general, our results demonstrated that lignocellulose-decomposing enzymes played a vital role in the formation of endophytes and their successful colonization of root tissues. This finding establishes a theoretical foundation for the development of broad-spectrum probiotics.
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Affiliation(s)
- Ting Zhang
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Juan Xiong
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Rongchuan Tian
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Ye Li
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qinyi Zhang
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ke Li
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiaohong Xu
- Library, Fujian Normal University, Fuzhou, China
| | - Lianming Liang
- Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Yi Zheng
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Baoyu Tian
- The Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
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12
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Qin W, Xia Y, Xiong Z, Song X, Ai L, Wang G. The intestinal colonization of Lactiplantibacillus plantarum AR113 is influenced by its mucins and intestinal environment. Food Res Int 2022; 157:111382. [DOI: 10.1016/j.foodres.2022.111382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
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13
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Kwon SK, Park JC, Kim KH, Yoon J, Cho Y, Lee B, Lee JJ, Jeong H, Oh Y, Kim SH, Lee SD, Hwang BR, Chung Y, Kim JF, Nam KT, Lee YC. Human gastric microbiota transplantation recapitulates premalignant lesions in germ-free mice. Gut 2022; 71:1266-1276. [PMID: 34389621 DOI: 10.1136/gutjnl-2021-324489] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/28/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Gastric cancer (GC) is a leading cause of cancer-related mortality. Although microbes besides Helicobacter pylori may also contribute to gastric carcinogenesis, wild-type germ-free (GF) mouse models investigating the role of human gastric microbiota in the process are not yet available. We aimed to evaluate the histopathological features of GF mouse stomachs transplanted with gastric microbiota from patients with different gastric disease states and their relationships with the microbiota. DESIGN Microbiota profiles in corpus and antrum tissues and gastric fluid from 12 patients with gastric dysplasia or GC were analysed. Thereafter, biopsied corpus and antrum tissues and gastric fluid from patients (n=15 and n=12, respectively) with chronic superficial gastritis, intestinal metaplasia or GC were inoculated into 42 GF C57BL/6 mice. The gastric microbiota was analysed by amplicon sequencing. Histopathological features of mouse stomachs were analysed immunohistochemically at 1 month after inoculation. An independent set of an additional 15 GF mice was also analysed at 1 year. RESULTS The microbial community structures of patients with dysplasia or GC in the corpus and antrum were similar. The gastric microbiota from patients with intestinal metaplasia or GC selectively colonised the mouse stomachs and induced premalignant lesions: loss of parietal cells and increases in inflammation foci, in F4/80 and Ki-67 expression, and in CD44v9/GSII lectin expression. Marked dysplastic changes were noted at 1 year post inoculation. CONCLUSION Major histopathological features of premalignant changes are reproducible in GF mice transplanted with gastric microbiota from patients with intestinal metaplasia or GC. Our results suggest that GF mice are useful for analysing the causality of associations reported in human gastric microbiome studies.
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Affiliation(s)
- Soon-Kyeong Kwon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.,Division of Applied Life Science (Brain Korea 21), Gyeongsang National University, Jinju, Republic of Korea
| | - Jun Chul Park
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kwang H Kim
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jaekyung Yoon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yejin Cho
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Buhyun Lee
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin-Jae Lee
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Life Science, Hallym University, Chuncheon, Republic of Korea
| | - Haengdueng Jeong
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yeseul Oh
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hee Kim
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - So Dam Lee
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Bo Ram Hwang
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yusook Chung
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea .,Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul, Republic of Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Chan Lee
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
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14
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Liu W, Sun Z, Ma C, Zhang J, Ma C, Zhao Y, Wei H, Huang S, Zhang H. Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice. Gut Microbes 2022; 13:1-13. [PMID: 33382948 PMCID: PMC7781656 DOI: 10.1080/19490976.2020.1830699] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Environmental exposure during earlier life stages can govern the assembly and development of gut microbiota, yet it is insufficiently understood. In this study, ex-germ-free mice were cohoused with distinct soil-microbiota (from desert, steppe, and forest) beddings within 60 days after birth and subsequently transferred to new soil beddings from 60 to 90th day. Using metagenomic shotgun sequencing, firstly, we found soil microbes from natural environments (birthplace) greatly influenced the gut community assembly in the housing experiment. About 27% microbial species and 12% functional components that associated with birthplaces at Day 60 were still discriminatory of birthplaces after transferring mice to new environments. Moreover, prior soil-exposure types are associated with the magnitude of temporal microbiome change due to environmental shifts. The appropriate soil-exposure (e.g., steppe) might help mice gut microbiome adapt to changing environments or host development. Our study demonstrated the continuous soil-exposure history earlier is associated with the gut microbiome individuality and development later.
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Affiliation(s)
- Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zheng Sun
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Chen Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiachao Zhang
- College of Food Science and Technology, Hainan University, Haikou, Hainan, China
| | - ChenChen Ma
- College of Food Science and Technology, Hainan University, Haikou, Hainan, China
| | - Yinqi Zhao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hong Wei
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China, Heping Zhang Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shi Huang
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China, Heping Zhang Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China, Heping Zhang Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
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15
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Lavoie C, Wellband K, Perreault A, Bernatchez L, Derome N. Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking. Microorganisms 2021; 9:microorganisms9091932. [PMID: 34576827 PMCID: PMC8465833 DOI: 10.3390/microorganisms9091932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/21/2022] Open
Abstract
In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of which exert long-term effects on host physiology. Therefore, our objective was to assess to what extent the resilience capacity of the microbiota of stocked salmon may prevent taxonomic convergence with that of their wild congeners after two months in the same natural environment. Using the 16S SSU rRNA marker gene, we tested the general hypothesis that environmental conditions during the very first steps of microbiota ontogeny imprint a permanent effect on later stages of microbiota recruitment. Our results first showed that gut microbiota composition of stocked and wild parr from the same genetic population, and sharing the same environment, was dependent on the early rearing environment. In contrast, skin microbiota in stocked individuals converged to that of wild individuals. Taxonomic composition and co-occurrence network analyses suggest an impairment of wild bacteria recruitment and a higher instability for the gut microbiota of stocked parr. This study is the first to demonstrate the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, raising the need to implement microbial ecology.
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Affiliation(s)
- Camille Lavoie
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Kyle Wellband
- Department of Biology, Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada;
| | - Alysse Perreault
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Louis Bernatchez
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Nicolas Derome
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-(418)-656-7726
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Kapustina Ž, Medžiūnė J, Alzbutas G, Rokaitis I, Matjošaitis K, Mackevičius G, Žeimytė S, Karpus L, Lubys A. High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts. Microb Genom 2021; 7. [PMID: 34473015 PMCID: PMC8715429 DOI: 10.1099/mgen.0.000624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. Neither approach is universally applicable, and the main efforts to resolve constraints have been devoted to improvement of computational prediction tools. Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1-V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. By in silico analysis of 13 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. Using mock communities and soil samples we experimentally validate st16S-seq and benchmark it against the established microbial classification techniques. We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing.
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Affiliation(s)
- Žana Kapustina
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania.,Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius 10257, Lithuania
| | - Justina Medžiūnė
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania.,Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, Vilnius 03225, Lithuania
| | - Gediminas Alzbutas
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | | | - Karolis Matjošaitis
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Gytis Mackevičius
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Simona Žeimytė
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Laurynas Karpus
- Biomatter Designs, Žirmūnų str. 139A, Vilnius 09120, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
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Wu Y, Zheng Y, Wang S, Chen Y, Tao J, Chen Y, Chen G, Zhao H, Wang K, Dong K, Hu F, Feng Y, Zheng H. Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis cerana and the Western honey bee Apis mellifera. J Adv Res 2021; 37:19-31. [PMID: 35499050 PMCID: PMC9039653 DOI: 10.1016/j.jare.2021.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/07/2021] [Accepted: 08/03/2021] [Indexed: 01/21/2023] Open
Abstract
The inter-species diversity of A. cerana and A. mellifera core gut bacteria was revealed. Core bacterial species of A. cerana and A. mellifera are distinctive in function. Functional profile of overall gut community of A. cerana and A. mellifera are similar. Metabolome showed that A. cerana and A. mellifera gut bacteria have similar metabolic capability. A. cerana and A. mellifera core gut bacteria have no strict host specificity.
Introduction The functional relevance of intra-species diversity in natural microbial communities remains largely unexplored. The guts of two closely related honey bee species, Apis cerana and A. mellifera, are colonised by a similar set of core bacterial species composed of host-specific strains, thereby providing a good model for an intra-species diversity study. Objectives We aim to assess the functional relevance of intra-species diversity of A. cerana and A. mellifera gut microbiota. Methods Honey bee workers were collected from four regions of China. Their gut microbiomes were investigated by shotgun metagenomic sequencing, and the bacterial compositions were compared at the species level. A cross-species colonisation assay was conducted, with the gut metabolomes being characterised by LC-MS/MS. Results Comparative analysis showed that the strain composition of the core bacterial species was host-specific. These core bacterial species presented distinctive functional profiles between the hosts. However, the overall functional profiles of the A. cerana and A. mellifera gut microbiomes were similar; this was further supported by the consistency of the honey bees’ gut metabolome, as the gut microbiota of different honey bee species showed rather similar metabolic profiles in the cross-species colonisation assay. Moreover, this experiment also demonstrated that the gut microbiota of A. cerana and A. mellifera could cross colonise between the two honey bee species. Conclusion Our findings revealed functional differences in most core gut bacteria between the guts of A. cerana and A. mellifera, which may be associated with their inter-species diversity. However, the functional profiles of the overall gut microbiomes between the two honey bee species converge, probably as a result of the overlapping ecological niches of the two species. Our findings provide critical insights into the evolution and functional roles of the mutualistic microbiota of honey bees and reveal that functional redundancy could stabilise the gene content diversity at the strain-level within the gut community.
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Affiliation(s)
- Yuqi Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yufei Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuai Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yanping Chen
- USDA-ARS Bee Research Laboratory, Beltsville, MD, USA
| | - Junyi Tao
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Yanan Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Gongwen Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hongxia Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Kai Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kun Dong
- Eastern Bee Research Institute, College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Fuliang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Corresponding authors.
| | - Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Corresponding authors.
| | - Huoqing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Corresponding authors.
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18
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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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19
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Xiao Y, Zhai Q, Zhang H, Chen W, Hill C. Gut Colonization Mechanisms of Lactobacillus and Bifidobacterium: An Argument for Personalized Designs. Annu Rev Food Sci Technol 2021; 12:213-233. [DOI: 10.1146/annurev-food-061120-014739] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lactobacillus and Bifidobacterium spp. are best understood for their applications as probiotics, which are often transient, but as commensals it is probable that stable colonization in the gut is important for their beneficial roles. Recent research suggests that the establishment and persistence of strains of Lactobacillus and Bifidobacterium in the gut are species- and strain-specific and affected by natural history, genomic adaptability, and metabolic interactions of the bacteria and the microbiome and immune aspects of the host but also regulated by diet. This provides new perspectives on the underlying molecular mechanisms. With an emphasis on host–microbe interaction, this review outlines how the characteristics of individual Lactobacillus and Bifidobacterium bacteria, the host genotype and microbiome structure,diet, and host–microbe coadaptation during bacterial gut transition determine and influence the colonization process. The diet-tuned and personally tailored colonization can be achieved via a machine learning prediction model proposed here.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
- Beijing Advanced Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Colin Hill
- School of Microbiology and APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
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Gheorghe CE, Ritz NL, Martin JA, Wardill HR, Cryan JF, Clarke G. Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls. Gut Microbes 2021; 13:1941711. [PMID: 34328058 PMCID: PMC8331043 DOI: 10.1080/19490976.2021.1941711] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/04/2023] Open
Abstract
In recent years, studies investigating the role of the gut microbiota in health and diseases have increased enormously - making it essential to deepen and question the research methodology employed. Fecal microbiota transplantation (FMT) in rodent studies (either from human or animal donors) allows us to better understand the causal role of the intestinal microbiota across multiple fields. However, this technique lacks standardization and requires careful experimental design in order to obtain optimal results. By comparing several studies in which rodents are the final recipients of FMT, we summarize the common practices employed. In this review, we document the limitations of this method and highlight different parameters to be considered while designing FMT Studies. Standardizing this method is challenging, as it differs according to the research topic, but avoiding common pitfalls is feasible. Several methodological questions remain unanswered to this day and we offer a discussion on issues to be explored in future studies.
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Affiliation(s)
- Cassandra E. Gheorghe
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jason A. Martin
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hannah R. Wardill
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
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21
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Li L, Fang Z, Liu Z, Zhao J, Zhang H, Wang S, He J, Lu W, Chen W. Lactobacillus reuteri CCFM1072 and CCFM1040 with the role of Treg cells regulation alleviate airway inflammation through modulating gut microbiota in allergic asthma mice. J Funct Foods 2021. [DOI: 10.1016/j.jff.2020.104286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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22
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Aluthge ND, Tom WA, Bartenslager AC, Burkey TE, Miller PS, Heath KD, Kreikemeier-Bower C, Kittana H, Schmaltz RJ, Ramer-Tait AE, Fernando SC. Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models. Commun Biol 2020; 3:760. [PMID: 33311550 PMCID: PMC7733510 DOI: 10.1038/s42003-020-01477-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better in the HMA piglets compared to HMA mice. Of interest was the greater transplantation success of members belonging to phylum Firmicutes in the HMA piglets compared to the HMA mice. Together, these results provide evidence for the HMA piglet model potentially being more broadly applicable for donors with more mature microbiotas while the HMA mouse model might be more relevant for developing microbiotas such as those of infants. This study also emphasizes the necessity to exercise caution in extrapolating findings from HMA animals to humans, since up to 28% of taxa from some donors failed to colonize either model.
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Affiliation(s)
- Nirosh D Aluthge
- Department of Animal Science, University of Nebraska-Lincoln, Animal Science Complex, 3940 Fair St., Lincoln, NE, 68583-0908, USA.,Department of Food Science and Technology, Food Innovation Center, University of Nebraska-Lincoln, 1901 N 21st St., Lincoln, NE, 68588-6205, USA
| | - Wesley A Tom
- Department of Animal Science, University of Nebraska-Lincoln, Animal Science Complex, 3940 Fair St., Lincoln, NE, 68583-0908, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Manter Hall, 1104 T St., Lincoln, NE, 68588-0118, USA
| | - Alison C Bartenslager
- Department of Animal Science, University of Nebraska-Lincoln, Animal Science Complex, 3940 Fair St., Lincoln, NE, 68583-0908, USA
| | - Thomas E Burkey
- Department of Animal Science, University of Nebraska-Lincoln, Animal Science Complex, 3940 Fair St., Lincoln, NE, 68583-0908, USA
| | - Phillip S Miller
- Department of Animal Science, University of Nebraska-Lincoln, Animal Science Complex, 3940 Fair St., Lincoln, NE, 68583-0908, USA
| | - Kelly D Heath
- Institutional Animal Care Program, University of Nebraska-Lincoln, 110 Mussehl Hall, 1915 N 38th St., Lincoln, NE, 68653-0720, USA
| | - Craig Kreikemeier-Bower
- Institutional Animal Care Program, University of Nebraska-Lincoln, 110 Mussehl Hall, 1915 N 38th St., Lincoln, NE, 68653-0720, USA
| | - Hatem Kittana
- Department of Food Science and Technology, Food Innovation Center, University of Nebraska-Lincoln, 1901 N 21st St., Lincoln, NE, 68588-6205, USA.,Veterinary Medical Diagnostic Laboratory (VMDL) at University of Missouri (MU), 901 E Campus Loop, Columbia, MO, 65211, USA
| | - Robert J Schmaltz
- Department of Food Science and Technology, Food Innovation Center, University of Nebraska-Lincoln, 1901 N 21st St., Lincoln, NE, 68588-6205, USA
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, Food Innovation Center, University of Nebraska-Lincoln, 1901 N 21st St., Lincoln, NE, 68588-6205, USA
| | - Samodha C Fernando
- Department of Animal Science, University of Nebraska-Lincoln, Animal Science Complex, 3940 Fair St., Lincoln, NE, 68583-0908, USA.
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23
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Xing J, Liu G, Zhang X, Bai D, Yu J, Li L, Wang X, Su S, Zhao Y, Bou G, Dugarjaviin M. The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys. Front Microbiol 2020; 11:596394. [PMID: 33343537 PMCID: PMC7744375 DOI: 10.3389/fmicb.2020.596394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/05/2020] [Indexed: 02/01/2023] Open
Abstract
The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3–V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age groups. In contrast to the adult donkeys, the gut microbiota diversity and richness of the young donkeys showed significantly less resemblance. The microbial data showed that diversity and richness increased with age, but a highly individual variation of microbial composition was observed at month 1. Principal coordinate analysis (PCoA) revealed a significant difference across five time points in the feces. The abundance of Bacteroides, Lactobacillus, and Odoribacter tended to decrease, while the proportion of Streptococcus was significantly increased with age. For functional prediction, the relative abundance of pathways had a significant difference in the feces across different age groups, for example, Terpenoids and Polyketides and Folding, Sorting, and Degradation (P < 0.05 or P < 0.01). The analysis of beta diversity (PCoA and LEfSe) and microbial functions predicted with PICRUSt (NSTIs) clearly divided the donkeys into foals (≤3 months old) and adults (≥7 months old). Microbial community composition and structure had distinctive features at each age group, in accordance with functional stability of the microbiota. Our findings established a framework for understanding the composition and function of the fecal microbiota to differ between young and adult donkeys.
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Affiliation(s)
- Jingya Xing
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Guiqin Liu
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China.,College of Agronomy, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng University, Liaocheng, China
| | - Xinzhuang Zhang
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongyi Bai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Jie Yu
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co., Ltd., Liaocheng, China
| | - Lanjie Li
- College of Agronomy, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng University, Liaocheng, China
| | - Xisheng Wang
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Shaofeng Su
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yiping Zhao
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Gerelchimeg Bou
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Manglai Dugarjaviin
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
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24
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Li N, Zuo B, Huang S, Zeng B, Han D, Li T, Liu T, Wu Z, Wei H, Zhao J, Wang J. Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation. MICROBIOME 2020; 8:161. [PMID: 33208178 PMCID: PMC7677849 DOI: 10.1186/s40168-020-00917-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microbiota transplantation. Feces as the excreted residue contain most of the large-intestinal microbes but lack small-intestinal microbes. We speculated that whole-intestinal microbiota transplantation (WIMT), comprising jejunal, ileal, cecal, and colonic microbiota, would be more effective for reshaping the entire intestinal microbiota than conventional fecal microbiota transplantation fecal microbiota transplantation (FMT). RESULTS We modeled the compartmentalized colonization of the gut microbiota via transplanting the microbiota from jejunum, ileum, cecum, and colon, respectively, into the germ-free mice. Transplanting jejunal or ileal microbiota induced more exogenous microbes' colonization in the small intestine (SI) of germ-free mice rather than the large intestine (LI), primarily containing Proteobacteria, Lactobacillaceae, and Cyanobacteria. Conversely, more saccharolytic anaerobes from exogenous cecal or colonic microbiota, such as Bacteroidetes, Prevotellaceae, Lachnospiraceae, and Ruminococcaceae, established in the LI of germ-free mice that received corresponding intestinal segmented microbiota transplantation. Consistent compartmentalized colonization patterns of microbial functions in the intestine of germ-free mice were also observed. Genes related to nucleotide metabolism, genetic information processing, and replication and repair were primarily enriched in small-intestinal communities, whereas genes associated with the metabolism of essential nutrients such as carbohydrates, amino acids, cofactors, and vitamins were mainly enriched in large-intestinal communities of germ-free mice. Subsequently, we compared the difference in reshaping the community structure of germ-free mice between FMT and WIMT. FMT mainly transferred LI-derived microorganisms and gene functions into the recipient intestine with sparse SI-derived microbes successfully transplanted. However, WIMT introduced more SI-derived microbes and associated microbial functions to the recipient intestine than FMT. Besides, WIMT also improved intestinal morphological development as well as reduced systematic inflammation responses of recipients compared with FMT. CONCLUSIONS Segmented exogenous microbiota transplantation proved the spatial heterogeneity of bacterial colonization along the gastrointestinal tract, i.e., the microbiota from one specific location selectively colonizes its homologous gut region. Given the lack of exogenous small-intestinal microbes during FMT, WIMT may be a promising alternative for conventional FMT to reconstitute the microbiota across the entire intestinal tract. Video Abstract.
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Affiliation(s)
- Na Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Bin Zuo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Shimeng Huang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038 China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Tiantian Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ting Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Zhenhua Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Hong Wei
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701 USA
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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25
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Wu Q, Chen T, El-Nezami H, Savidge TC. Food ingredients in human health: Ecological and metabolic perspectives implicating gut microbiota function. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study. Sci Rep 2020; 10:7350. [PMID: 32355187 PMCID: PMC7192945 DOI: 10.1038/s41598-020-64393-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
To better understand the evolutionary significance of symbiotic interactions in nature, microbiome studies can help to identify the ecological factors that may shape host-associated microbial communities. In this study we explored both 16S and 18S rRNA microbial communities of D. armigerum from both wild caught individuals collected in the Amazon and individuals kept in the laboratory and fed on controlled diets. We also investigated the role of colony, sample type, development and caste on structuring microbial communities. Our bacterial results (16S rRNA) reveal that (1) there are colony level differences between bacterial communities; (2) castes do not structure communities; (3) immature stages (brood) have different bacterial communities than adults; and 4) individuals kept in the laboratory with a restricted diet showed no differences in their bacterial communities from their wild caught nest mates, which could indicate the presence of a stable and persistent resident bacterial community in this host species. The same categories were also tested for microbial eukaryote communities (18S rRNA), and (5) developmental stage has an influence on the diversity recovered; (6) the diversity of taxa recovered has shown this can be an important tool to understand additional aspects of host biology and species interactions.
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27
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Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J. Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. Cell 2020; 180:454-470.e18. [PMID: 32004459 PMCID: PMC7192218 DOI: 10.1016/j.cell.2020.01.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/06/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022]
Abstract
Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.
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Affiliation(s)
- Wei Zhou
- The Jackson Laboratory, Farmington, CT, USA
| | | | | | | | | | | | | | - Julia Oh
- The Jackson Laboratory, Farmington, CT, USA.
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28
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Liu H, Zeng X, Zhang G, Hou C, Li N, Yu H, Shang L, Zhang X, Trevisi P, Yang F, Liu Z, Qiao S. Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut. BMC Biol 2019; 17:106. [PMID: 31852478 PMCID: PMC6921401 DOI: 10.1186/s12915-019-0729-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The early-life microbiota exerts a profound and lifelong impact on host health. Longitudinal studies in humans have been informative but are mostly based on the analysis of fecal samples and cannot shed direct light on the early development of mucosa-associated intestinal microbiota and its impact on GI function. Using piglets as a model for human infants, we assess here the succession of mucosa-associated microbiota across the intestinal tract in the first 35 days after birth. RESULTS Although sharing a similar composition and predicted functional profile at birth, the mucosa-associated microbiome in the small intestine (jejunum and ileum) remained relatively stable, while that of the large intestine (cecum and colon) quickly expanded and diversified by day 35. Among detected microbial sources (milk, vagina, areolar skin, and feces of sows, farrowing crate, and incubator), maternal milk microbes were primarily responsible for the colonization of the small intestine, contributing approximately 90% bacteria throughout the first 35 days of the neonatal life. Although maternal milk microbes contributed greater than 90% bacteria to the large intestinal microbiota of neonates upon birth, their presence gradually diminished, and they were replaced by maternal fecal microbes by day 35. We found strong correlations between the relative abundance of specific mucosa-associated microbes, particularly those vertically transmitted from the mother, and the expression levels of multiple intestinal immune and barrier function genes in different segments of the intestinal tract. CONCLUSION We revealed spatially specific trajectories of microbial colonization of the intestinal mucosa in the small and large intestines, which can be primarily attributed to the colonization by vertically transmitted maternal milk and intestinal microbes. Additionally, these maternal microbes may be involved in the establishment of intestinal immune and barrier functions in neonates. Our findings strengthen the notion that studying fecal samples alone is insufficient to fully understand the co-development of the intestinal microbiota and immune system and suggest the possibility of improving neonatal health through the manipulation of maternal microbiota.
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Affiliation(s)
- Hongbin Liu
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China
- Present Address: Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Li
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China
| | - Lijun Shang
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China
| | - Xiaoya Zhang
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China
| | - Paolo Trevisi
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Feiyun Yang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Zuohua Liu
- Chongqing Academy of Animal Science, Chongqing, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition and Beijing Key Laboratory of Bio-Feed Additives, China Agricultural University, Beijing, China.
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29
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Leystra AA, Clapper ML. Gut Microbiota Influences Experimental Outcomes in Mouse Models of Colorectal Cancer. Genes (Basel) 2019; 10:genes10110900. [PMID: 31703321 PMCID: PMC6895921 DOI: 10.3390/genes10110900] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Mouse models are a valuable resource for use throughout the development and testing of new therapeutic strategies for CRC. Tumorigenesis and response to therapy in humans and mouse models alike are influenced by the microbial communities that colonize the gut. Differences in the composition of the gut microbiota can confound experimental findings and reduce the replicability and translatability of the resulting data. Despite this, the contribution of resident microbiota to preclinical tumor models is often underappreciated. This review does the following: (1) summarizes evidence that the gut microbiota influence CRC disease phenotypes; (2) outlines factors that can influence the composition of the gut microbiota; and (3) provides strategies that can be incorporated into the experimental design, to account for the influence of the microbiota on intestinal phenotypes in mouse models of CRC. Through careful experimental design and documentation, mouse models can continue to rapidly advance efforts to prevent and treat colon cancer.
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30
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Wang S, Ryan CA, Boyaval P, Dempsey EM, Ross RP, Stanton C. Maternal Vertical Transmission Affecting Early-life Microbiota Development. Trends Microbiol 2019; 28:28-45. [PMID: 31492538 DOI: 10.1016/j.tim.2019.07.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/10/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
Abstract
The association of the human microbiome with health outcomes has attracted much interest toward its therapeutic manipulation. The likelihood of modulating the human microbiome in early life is high and offers great potential to exert profound effects on human development since the early microbiota shows more flexibility compared to that of adults. The human microbiota, being similar to human genetics, can be transmitted from mother to infant, providing insights into early microbiota acquisition, subsequent development, and potential opportunities for intervention. Here, we review adaptations of the maternal microbiota during pregnancy, birth, and infancy, the acquisition and succession of early-life microbiota, and highlight recent efforts to elucidate mother-to-infant microbiota transmission. We further discuss how the mother-to-infant microbial transmission is shaped; and finally we address potential directions for future studies to promote our understanding within this field.
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Affiliation(s)
- Shaopu Wang
- APC Microbiome Ireland, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - C Anthony Ryan
- APC Microbiome Ireland, Cork, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | | | - Eugene M Dempsey
- APC Microbiome Ireland, Cork, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland; INFANT Centre, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Cork, Ireland; College of Science Engineering and Food Science, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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Daharsh L, Zhang J, Ramer-Tait A, Li Q. A Double Humanized BLT-mice Model Featuring a Stable Human-Like Gut Microbiome and Human Immune System. J Vis Exp 2019. [PMID: 31524867 DOI: 10.3791/59773] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Humanized mice (hu-mice) that feature a functional human immune system have fundamentally changed the study of human pathogens and disease. They can be used to model diseases that are otherwise difficult or impossible to study in humans or other animal models. The gut microbiome can have a profound impact on human health and disease. However, the murine gut microbiome is very different than the one found in humans. There is a need for improved pre-clinical hu-mice models that have an engrafted human gut microbiome. Therefore, we created double hu-mice that feature both a human immune system and stable human-like gut microbiome. NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice are one of the best animals for humanization due to their high level of immunodeficiency. However, germ-free NSG mice, and various other important germ-free mice models are not currently commercially available. Further, many research settings do not have access to gnotobiotic facilities, and working under gnotobiotic conditions can often be expensive and time consuming. Importantly, germ-free mice have several immune deficiencies that exist even after the engraftment of microbes. Therefore, we developed a protocol that does not require germ-free animals or gnotobiotic facilities. To generate double hu-mice, NSG mice were treated with radiation prior to surgery to create bone-marrow, liver, thymus-humanized (hu-BLT) mice. The mice were then treated with broad spectrum antibiotics to deplete the pre-existing murine gut microbiome. After antibiotic treatment, the mice were given fecal transplants with healthy human donor samples via oral gavage. Double hu-BLT mice had unique 16S rRNA gene profiles based on the individual human donor sample that was transplanted. Importantly, the transplanted human-like microbiome was stable in the double hu-BLT mice for the duration of the study up to 14.5 weeks post-transplant.
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Affiliation(s)
- Lance Daharsh
- Nebraska Center for Virology; School of Biological Sciences, University of Nebraska-Lincoln
| | - Jianshui Zhang
- Nebraska Center for Virology; School of Biological Sciences, University of Nebraska-Lincoln
| | - Amanda Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln
| | - Qingsheng Li
- Nebraska Center for Virology; School of Biological Sciences, University of Nebraska-Lincoln;
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Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC. Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci U S A 2019; 116:12804-12809. [PMID: 31186361 PMCID: PMC6600964 DOI: 10.1073/pnas.1900102116] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.
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Affiliation(s)
- Jared Kehe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anthony Kulesa
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anthony Ortiz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Sri Gowtham Thakku
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Health Sciences and Technology, MIT and Harvard, Cambridge, MA 02139
| | - Daniel Sellers
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155
| | - Seppe Kuehn
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel 76100
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
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Feng P, Ye Z, Kakade A, Virk AK, Li X, Liu P. A Review on Gut Remediation of Selected Environmental Contaminants: Possible Roles of Probiotics and Gut Microbiota. Nutrients 2018; 11:nu11010022. [PMID: 30577661 PMCID: PMC6357009 DOI: 10.3390/nu11010022] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
Various environmental contaminants including heavy metals, pesticides and antibiotics can contaminate food and water, leading to adverse effects on human health, such as inflammation, oxidative stress and intestinal disorder. Therefore, remediation of the toxicity of foodborne contaminants in human has become a primary concern. Some probiotic bacteria, mainly Lactobacilli, have received a great attention due to their ability to reduce the toxicity of several contaminants. For instance, Lactobacilli can reduce the accumulation and toxicity of selective heavy metals and pesticides in animal tissues by inhibiting intestinal absorption of contaminants and enhancing intestinal barrier function. Probiotics have also shown to decrease the risk of antibiotic-associated diarrhea possibly via competing and producing antagonistic compounds against pathogenic bacteria. Furthermore, probiotics can improve immune function by enhancing the gut microbiota mediated anti-inflammation. Thus, these probiotic bacteria are promising candidates for protecting body against foodborne contaminants-induced toxicity. Study on the mechanism of these beneficial bacterial strains during remediation processes and particularly their interaction with host gut microbiota is an active field of research. This review summarizes the current understanding of the remediation mechanisms of some probiotics and the combined effects of probiotics and gut microbiota on remediation of foodborne contaminants in vivo.
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Affiliation(s)
- Pengya Feng
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
| | - Ze Ye
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
| | - Apurva Kakade
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
| | - Amanpreet Kaur Virk
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
| | - Xiangkai Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
| | - Pu Liu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China.
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