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Sariyati NH, Othman N, Abdullah-Fauzi NAF, Chan E, Md-Zain BM, Karuppannan KV, Abdul-Latiff MAB. Characterizing the gastrointestinal microbiome diversity in endangered Malayan Siamang (Symphalangus syndactylus): Insights into group composition, age variability and sex-related patterns. J Med Primatol 2024; 53:e12730. [PMID: 39148344 DOI: 10.1111/jmp.12730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus. METHODS This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region. RESULTS A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut. CONCLUSIONS This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.
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Affiliation(s)
- Nur Hartini Sariyati
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Eddie Chan
- Treks Event Sdn Bhd, Lot AW/G5.00, GF, Awana Hotel Genting Highlands Resort, Genting Highlands, Pahang, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
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Flynn JK, Ortiz AM, Vujkovic-Cvijin I, Welles HC, Simpson J, Castello Casta FM, Yee DS, Rahmberg AR, Brooks KL, De Leon M, Knodel S, Birse K, Noel-Romas L, Deewan A, Belkaid Y, Burgener A, Brenchley JM. Translocating bacteria in SIV infection are not stochastic and preferentially express cytosine methyltransferases. Mucosal Immunol 2024; 17:1089-1101. [PMID: 39089468 DOI: 10.1016/j.mucimm.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Microbial translocation is a significant contributor to chronic inflammation in people living with HIV (PLWH) and is associated with increased mortality and morbidity in individuals treated for long periods with antiretrovirals. The use of therapeutics to treat microbial translocation has yielded mixed effects, in part, because the species and mechanisms contributing to translocation in HIV remain incompletely characterized. To characterize translocating bacteria, we cultured translocators from chronically SIV-infected rhesus macaques. Proteomic profiling of these bacteria identified cytosine-specific methyltransferases as a common feature and therefore, a potential driver of translocation. Treatment of translocating bacteria with the cytosine methyltransferase inhibitor decitabine significantly impaired growth for several species in vitro. In rhesus macaques, oral treatment with decitabine led to some transient decreases in translocator taxa in the gut microbiome. These data provide mechanistic insight into bacterial translocation in lentiviral infection and explore a novel therapeutic intervention that may improve the prognosis of PLWH.
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Affiliation(s)
- Jacob K Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA
| | - Hugh C Welles
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA
| | - Jennifer Simpson
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | | | - Debra S Yee
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Kelsie L Brooks
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Marlon De Leon
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Samantha Knodel
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Kenzie Birse
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Laura Noel-Romas
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Anshu Deewan
- Integrated Data Sciences Section, Research Technologies Branch, NIAID, NIH, Bethesda, MD, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA; Metaorganism Unit, Immunology Department, Institut Pasteur, 75724 Paris, France
| | - Adam Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada; Department of Medicine Solna, Karolinksa Institutet, Stockholm, Sweden
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA.
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Maaskant A, Voermans B, Levin E, de Goffau MC, Plomp N, Schuren F, Remarque EJ, Smits A, Langermans JAM, Bakker J, Montijn R. Microbiome signature suggestive of lactose-intolerance in rhesus macaques (Macaca mulatta) with intermittent chronic diarrhea. Anim Microbiome 2024; 6:53. [PMID: 39313845 PMCID: PMC11421201 DOI: 10.1186/s42523-024-00338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Chronic diarrhea is a common cause of mortality and morbidity in captive rhesus macaques (Macaca mulatta). The exact etiology of chronic diarrhea in macaques remains unidentified. The occurrence of diarrhea is frequently linked to dysbiosis within the gut microbiome. Research into microbiome signatures correlated with diarrhea in macaques have predominantly been conducted with single sample collections. Our analysis was based on the metagenomic composition of longitudinally acquired fecal samples from rhesus macaques with chronic diarrhea and clinically healthy rhesus macaques that were obtained over the course of two years. We aimed to investigate potential relationships between the macaque gut microbiome, the presence of diarrhea and diet interventions with a selection of commercially available monkey diets. RESULTS The microbiome signature of macaques with intermittent chronic diarrhea showed a significant increase in lactate producing bacteria e.g. lactobacilli, and an increase in fermenters of lactate and succinate. Strikingly, two lactose free diets were associated with a lower incidence of diarrhea. CONCLUSION A lactose intolerance mechanism is suggested in these animals by the bloom of Lactobacillus in the presence of lactose resulting in an overproduction of intermediate fermentation products likely led to osmotically induced diarrhea. This study provides new insights into suspected microbiome-lactose intolerance relationship in rhesus macaques with intermittent chronic diarrhea. The integration of machine learning with metagenomic data analysis holds potential for developing targeted dietary interventions and therapeutic strategies and therefore ensuring a healthier and more resilient primate population.
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Affiliation(s)
- Annemiek Maaskant
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
- Department Population Health Sciences, Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Heidelberglaan 8, 3584 CM, Utrecht, The Netherlands.
| | - Bas Voermans
- HORAIZON Technology BV, Marshallaan 2, 2625 GZ, Delft, The Netherlands.
- Department of Vascular Medicine, Amsterdam UMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Evgeni Levin
- HORAIZON Technology BV, Marshallaan 2, 2625 GZ, Delft, The Netherlands
| | - Marcus C de Goffau
- HORAIZON Technology BV, Marshallaan 2, 2625 GZ, Delft, The Netherlands
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Nicole Plomp
- Department of Microbiology and Systems Biology, Organization for Applied Scientific Research (TNO), Sylviusweg 71, 2333 BE, Leiden, The Netherlands
| | - Frank Schuren
- Department of Microbiology and Systems Biology, Organization for Applied Scientific Research (TNO), Sylviusweg 71, 2333 BE, Leiden, The Netherlands
| | - Edmond J Remarque
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Antoine Smits
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Jan A M Langermans
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
- Department Population Health Sciences, Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Heidelberglaan 8, 3584 CM, Utrecht, The Netherlands
| | - Jaco Bakker
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Roy Montijn
- Department of Microbiology and Systems Biology, Organization for Applied Scientific Research (TNO), Sylviusweg 71, 2333 BE, Leiden, The Netherlands
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Lippincott RA, O’Connor J, Neff CP, Lozupone C, Palmer BE. Deciphering HIV-associated inflammation: microbiome's influence and experimental insights. Curr Opin HIV AIDS 2024; 19:228-233. [PMID: 38884255 PMCID: PMC11305906 DOI: 10.1097/coh.0000000000000866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
PURPOSE OF REVIEW To review novel experimental approaches for studying host:microbe interactions and their role in intestinal and systemic inflammation in people living with HIV (PLWH). RECENT FINDINGS Inflammation in PLWH is impacted by interactions between the microbiome, the intestinal epithelium, and immune cells. This complex interplay is not fully understood and requires a variety of analytical techniques to study. Using a multiomic systems biology approach provides hypothesis generating data on host:microbe interactions that can be used to guide further investigation. The direct interactions between host cells and microbes can be elucidated using peripheral blood mononuclear cells (PBMCs), lamina propria mononuclear cells (LPMC's) or human intestinal organoids (HIO). Additionally, the broader relationship between the host and the microbiome can be explored using animal models such as nonhuman primates and germ-free and double humanized mice. SUMMARY To explore complex host:microbe relationships, hypotheses are generated and investigations are guided by multiomic data, while causal components are identified using in-vitro and in-vivo assays.
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Affiliation(s)
| | - John O’Connor
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Ortiz AM, Brenchley JM. Untangling the role of the microbiome across the stages of HIV disease. Curr Opin HIV AIDS 2024; 19:221-227. [PMID: 38935047 PMCID: PMC11305932 DOI: 10.1097/coh.0000000000000870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW The primate microbiome consists of bacteria, eukaryotes, and viruses that dynamically shape and respond to host health and disease. Understanding how the symbiotic relationship between the host and microbiome responds to HIV has implications for therapeutic design. RECENT FINDINGS Advances in microbiome identification technologies have expanded our ability to identify constituents of the microbiome and to infer their functional capacity. The dual use of these technologies and animal models has allowed interrogation into the role of the microbiome in lentiviral acquisition, vaccine efficacy, and the response to antiretrovirals. Lessons learned from such studies are now being harnessed to design microbiome-based interventions. SUMMARY Previous studies considering the role of the microbiome in people living with HIV largely described viral acquisition as an intrusion on the host:microbiome interface. Re-framing this view to consider HIV as a novel, albeit unwelcome, component of the microbiome may better inform the research and development of pre and postexposure prophylaxes.
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Affiliation(s)
- Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland, USA
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6
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Brenchley JM, Serrano-Villar S. From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy. MICROBIOME 2024; 12:113. [PMID: 38907315 PMCID: PMC11193286 DOI: 10.1186/s40168-024-01825-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV. RESULTS Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents. CONCLUSIONS Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, MA, USA.
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, IRYCIS and CIBERInfec, Madrid, Spain.
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7
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Meng P, Zhang G, Ma X, Ding X, Song X, Dang S, Yang R, Xu L. Characterization of intestinal fungal community diversity in people living with HIV/AIDS (PLWHA). AIDS Res Ther 2024; 21:10. [PMID: 38350942 PMCID: PMC10863270 DOI: 10.1186/s12981-023-00589-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 02/15/2024] Open
Abstract
Acquired Immune Deficiency Syndrome (AIDS) is a highly dangerous infectious disease caused by the Human Immunodeficiency Virus (HIV), a virus that attacks the human immune system. To explore the correlation between intestinal fungal community and immune function (Immune cells and inflammatory factors) in people living with HIV/AIDS (PLWHA). The feces and blood samples were collected from two groups of subjects: PLWHA and healthy controls. High-throughput sequencing of the internal transcribed spacer 1, flow cytometry, and ELISA were performed to analyze the differences and correlations between fungal microbiota, cellular immune status and serum inflammatory factors in the two groups. There were significant differences in the composition of fungal microbiota between the two groups. The relative abundance of Candida, Bjerkandera, and Xeromyces in PLWHA was significantly higher than that of healthy volunteers (P < 0.01), while the relative abundance of Mycospaerella, Xeroxysium, Penicillium, and Glomerella in PLWHA was significantly lower than that of healthy volunteers. The correlation analysis results show that Mycospaerella and Xeromyces are significantly positively correlated with CD4+/CD8+ T cells and the anti-inflammatory cytokine IL-4. On the other hand, Candida was positively correlated with pro-inflammatory factors negatively correlated with CD4+/CD8+ T cells and the anti-inflammatory cytokine IL-4, while it is positively correlated with pro-inflammatory cytokines. The significant increase in the relative abundance of Candida may be one of the important causes of intestinal damage in PLWHA. The results of this study contribute to the understanding of the relationship between fungal microbiota structure and immune function in the gut ecology of PLWHA.
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Affiliation(s)
- Pengfei Meng
- Henan University of Chinese Medicine, Zhengzhou, 450000, China
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Guichun Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Xiuxia Ma
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Xue Ding
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Xiyuan Song
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Shuyuan Dang
- Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Ruihan Yang
- Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Liran Xu
- Henan University of Chinese Medicine, Zhengzhou, 450000, China.
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China.
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J, Schülke O. The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels. MICROBIOME 2023; 11:165. [PMID: 37501202 PMCID: PMC10373267 DOI: 10.1186/s40168-023-01596-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/11/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. RESULTS In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. CONCLUSIONS In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.
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Affiliation(s)
- Simone Anzà
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany.
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Michael Heistermann
- Endocrinology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Somboon Sangmaneedet
- Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Julia Ostner
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Oliver Schülke
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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Li C, Zhang X. Current in Vitro and Animal Models for Understanding Foods: Human Gut-Microbiota Interactions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12733-12745. [PMID: 36166347 DOI: 10.1021/acs.jafc.2c04238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The food-gut microbiota interaction is an important regulator of human health. Numerous in vitro and animal models have thus been developed in order to simulate the specific food-gut microbiota and/or host-gut microbiota interactions in the human colon. This review summarizes the design principles of each model and discusses their advantages and weaknesses in terms of studying food-gut microbiota interactions. In vitro fermentation models appear to be reliable methods to investigate various aspects involved in the food-gut microbiota interactions in humans. However, many physiological perspectives lack appreciation of these models, such as peristaltic movement, biochemical conditions, and gastrointestinal anatomy. Animal models provide more physiological relevance to human trials compared to in vitro models. However, they may have gastrointestinal tract aspects that are distinct from human subjects. This review contains important information that can help the development of more advanced models to study food-gut microbiota interactions in humans.
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Affiliation(s)
- Cheng Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Joint International Research Laboratory of Agriculture Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xiaowei Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
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Chin N, Narayan NR, Méndez-Lagares G, Ardeshir A, Chang WLW, Deere JD, Fontaine JH, Chen C, Kieu HT, Lu W, Barry PA, Sparger EE, Hartigan-O'Connor DJ. Cytomegalovirus infection disrupts the influence of short-chain fatty acid producers on Treg/Th17 balance. MICROBIOME 2022; 10:168. [PMID: 36210471 PMCID: PMC9549678 DOI: 10.1186/s40168-022-01355-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Both the gut microbiota and chronic viral infections have profound effects on host immunity, but interactions between these influences have been only superficially explored. Cytomegalovirus (CMV), for example, infects approximately 80% of people globally and drives significant changes in immune cells. Similarly, certain gut-resident bacteria affect T-cell development in mice and nonhuman primates. It is unknown if changes imposed by CMV on the intestinal microbiome contribute to immunologic effects of the infection. RESULTS We show that rhesus cytomegalovirus (RhCMV) infection is associated with specific differences in gut microbiota composition, including decreased abundance of Firmicutes, and that the extent of microbial change was associated with immunologic changes including the proliferation, differentiation, and cytokine production of CD8+ T cells. Furthermore, RhCMV infection disrupted the relationship between short-chain fatty acid producers and Treg/Th17 balance observed in seronegative animals, showing that some immunologic effects of CMV are due to disruption of previously existing host-microbe relationships. CONCLUSIONS Gut microbes have an important influence on health and disease. Diet is known to shape the microbiota, but the influence of concomitant chronic viral infections is unclear. We found that CMV influences gut microbiota composition to an extent that is correlated with immunologic changes in the host. Additionally, pre-existing correlations between immunophenotypes and gut microbes can be subverted by CMV infection. Immunologic effects of CMV infection on the host may therefore be mediated by two different mechanisms involving gut microbiota. Video Abstract.
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Affiliation(s)
- Ning Chin
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Nicole R Narayan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Gema Méndez-Lagares
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, Davis, USA
| | - W L William Chang
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Jesse D Deere
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Justin H Fontaine
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Connie Chen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Hung T Kieu
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Wenze Lu
- California National Primate Research Center, University of California, Davis, Davis, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA
| | - Peter A Barry
- Center for Immunology and Infectious Diseases, University of California, Davis, Davis, USA
| | - Ellen E Sparger
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, USA
| | - Dennis J Hartigan-O'Connor
- California National Primate Research Center, University of California, Davis, Davis, USA.
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, USA.
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, USA.
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12
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Lavinder TR, Fachko DN, Stanton J, Varco-Merth B, Smedley J, Okoye AA, Skalsky RL. Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques ( Macaca mulatta). Comp Med 2022; 72:287-297. [PMID: 36162961 PMCID: PMC9827599 DOI: 10.30802/aalas-cm-22-000020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
HIV-infected people develop reproducible disruptions in their gastrointestinal microbiota. Despite the suppression of HIV viremia via long-term antiretroviral therapy (ART), alterations still occur in gut microbial diversity and the commensal microbiota. Mounting evidence suggests these microbial changes lead to the development of gut dysbiosis-persistent inflammation that damages the gut mucosa-and correlate with various immune defects. In this study, we examined how early ART intervention influences microbial diversity in SIV-infected rhesus macaques. Using 16S rRNA sequencing, we defined the fecal microbiome in macaques given daily ART beginning on either 3 or 7 d after SIV infection (dpi) and characterized changes in composition, α diversity, and β diversity from before infection through 112 dpi. The dominant phyla in the fecal samples before infection were Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria. After SIV infection and ART, the relative abundance of Firmicutes and Bacteroidetes did not change significantly. Significant reductions in α diversity occurred across time when ART was initiated at 3 dpi but not at 7 dpi. Principal coordinate analysis of samples revealed a divergence in β diversity in both treatment groups after SIV infection, with significant differences depending on the timing of ART administration. These results indicate that although administration of ART at 3 or 7 dpi did not substantially alter fecal microbial composition, the timing of early ART measurably altered phylogenetic diversity.
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Affiliation(s)
- Tiffany R Lavinder
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University,,Corresponding authors. ,
| | - Devin N Fachko
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and
| | - Jeffrey Stanton
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Afam A Okoye
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon,Corresponding authors. ,
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13
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Vujkovic-Cvijin I, Welles HC, Ha CWY, Huq L, Mistry S, Brenchley JM, Trinchieri G, Devkota S, Belkaid Y. The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces. Sci Transl Med 2022; 14:eabl3927. [PMID: 35976997 PMCID: PMC9741845 DOI: 10.1126/scitranslmed.abl3927] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Unique gut microbiota compositions have been associated with inflammatory diseases, but identifying gut bacterial functions linked to immune activation in humans remains challenging. Translocation of pathogens from mucosal surfaces into peripheral tissues can elicit immune activation, although whether and which gut commensal bacteria translocate in inflammatory diseases is difficult to assess. We report that a subset of commensal gut microbiota constituents that translocate across the gut barrier in mice and humans are associated with heightened systemic immunoglobulin G (IgG) responses. We present a modified high-throughput, culture-independent approach to quantify systemic IgG against gut commensal bacteria in human serum samples without the need for paired stool samples. Using this approach, we highlight several commensal bacterial species that elicit elevated IgG responses in patients with inflammatory bowel disease (IBD) including taxa within the clades Collinsella, Bifidobacterium, Lachnospiraceae, and Ruminococcaceae. These and other taxa identified as translocating bacteria or targets of systemic immunity in IBD concomitantly exhibited heightened transcriptional activity and growth rates in IBD patient gut microbiomes. Our approach represents a complementary tool to illuminate interactions between the host and its gut microbiota and may provide an additional method to identify microbes linked to inflammatory disease.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Hugh C. Welles
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Connie W. Y. Ha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lutfi Huq
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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14
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Guo J, Song C, Liu Y, Wu X, Dong W, Zhu H, Xiang Z, Qin C. Characteristics of gut microbiota in representative mice strains: Implications for biological research. Animal Model Exp Med 2022; 5:337-349. [PMID: 35892142 PMCID: PMC9434578 DOI: 10.1002/ame2.12257] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Background Experimental animals are used to study physiological phenomena, pathological mechanisms, and disease prevention. The gut microbiome is known as a potential confounding factor for inconsistent data from preclinical studies. Although many gut microbiome studies have been conducted in recent decades, few have focused on gut microbiota fluctuation among representative mouse strains. Methods A range of frequently used mouse strains were selected from 34 isolation packages representing disease‐related animal (DRA), immunity defect animal (IDA), or gene‐editing animal (GEA) from the BALB/c and C57BL/6J backgrounds together with normal mice, and their microbial genomic DNA were isolated from mouse feces to sequence for the exploration of gut microbiota. Results Mouse background strain, classification, introduced source, introduced year, and reproduction type significantly affected the gut microbiota structure (p < 0.001 for all parameters), with background strain contributing the greatest influence (R2 = 0.237). In normal groups, distinct gut microbiota types existed in different mouse strains. Sixty‐four core operational taxonomic units were obtained from normal mice, and 12 belonged to Lactobacillus. Interestingly, the gut microbiota in C57BL/6J was more stable than that in BALB/c mice. Furthermore, the gut microbiota in the IDA, GEA, and DRA groups significantly differed from that in normal groups (p < 0.001 for all). Compared with the normal group, there was a significantly higher Chao1 and Shannon index (p < 0.001 for all) in the IDA, GEA, and DRA groups. Markedly changed classes occurred with Firmicutes and Bacteroidetes. The abundances of Helicobacter, Blautia, Enterobacter, Bacillus, Clostridioides, Paenibacillus, and Clostridiales all significantly decreased in the IDA, GEA, and DRA groups, whereas those of Saccharimonas, Rikenella, and Odoribacter all significantly increased.
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Affiliation(s)
- Jianguo Guo
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Chenchen Song
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Yunbo Liu
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Xuying Wu
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Wei Dong
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Hua Zhu
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Zhiguang Xiang
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
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15
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Johnson AL, Keesler RI, Lewis AD, Reader JR, Laing ST. Common and Not-So-Common Pathologic Findings of the Gastrointestinal Tract of Rhesus and Cynomolgus Macaques. Toxicol Pathol 2022; 50:638-659. [PMID: 35363082 PMCID: PMC9308647 DOI: 10.1177/01926233221084634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rhesus and cynomolgus macaques are the most frequently used nonhuman primate (NHP) species for biomedical research and toxicology studies of novel therapeutics. In recent years, there has been a shortage of laboratory macaques due to a variety of competing factors. This was most recently exacerbated by the surge in NHP research required to address the severe acute respiratory syndrome (SARS)-coronavirus 2 pandemic. Continued support of these important studies has required the use of more varied cohorts of macaques, including animals with different origins, increased exposure to naturally occurring pathogens, and a wider age range. Diarrhea and diseases of the gastrointestinal tract are the most frequently occurring spontaneous findings in macaques of all origins and ages. The purpose of this review is to alert pathologists and scientists involved in NHP research to these findings and their impact on animal health and study endpoints, which may otherwise confound the interpretation of data generated using macaques.
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Affiliation(s)
| | | | - Anne D Lewis
- Oregon National Primate Research Center, Beaverton, Oregon, USA
| | - J Rachel Reader
- California National Primate Research Center, Davis, California, USA
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16
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Teng Y, Yang X, Li G, Zhu Y, Zhang Z. Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest. Front Microbiol 2022; 13:811990. [PMID: 35197954 PMCID: PMC8859092 DOI: 10.3389/fmicb.2022.811990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota play a significant role for animals to adapt to the changing environment. Host species and habitats are key drivers in shaping the diversity and composition of the microbiota, but the determinants of composition of the sympatric host gut microbiome remain poorly understood within an ecosystem. In this study, we examined the effects of habitats of different succession stages and host species on the diversity and composition of fecal gut microbiota in four sympatric rodent species (Apodemus draco, Leopoldamys edwardsi, Niviventer confucianus, and Niviventer fulvescens) in a subtropical forest. We found, as compared to the differences between species, habitat types showed a much larger effect on the gut microbiota of rodents. Alpha diversity of the microbial community of A. draco, N. fulvescens, and N. confucianus was highest in farmland, followed by primary forest and shrubland, and lowest in secondary forest. Beta diversity of the three rodent species showed significant different among habitats. The alpha diversity of gut microbiota of L. edwardsi was significantly higher than those of A. draco and N. confucianus, and its beta diversity showed significant difference from A. draco. Our results suggested that gut microbiota were important for animals in responding to diet changes in different habitats under human disturbances.
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Affiliation(s)
- Yuwei Teng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xifu Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yunlong Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Zhibin Zhang,
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17
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Adams NE, Becker MA, Edmands S. Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox. Front Microbiol 2021; 12:748323. [PMID: 34925262 PMCID: PMC8672056 DOI: 10.3389/fmicb.2021.748323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.
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Affiliation(s)
- Nicole E Adams
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Madeleine A Becker
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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18
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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Propensity score-matched comparison between totally laparoscopic right hemicolectomy with transcolonic natural orifice specimen extraction and conventional laparoscopic surgery with mini-laparotomy in the treatment of ascending colon cancer (with video). Gastrointest Endosc 2021; 94:642-650. [PMID: 33798538 DOI: 10.1016/j.gie.2021.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/21/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Now that the debate about the safety and effectiveness of laparoscopic versus open surgery is over, attention has turned to innovations that can verify whether minimizing the impact of laparoscopy on the abdominal wall can further reduce pain, improve patient comfort, lead to superior cosmesis, and reduce morbidity. The aim of this study was to further explore the application value of totally laparoscopic right hemicolectomy with transcolonic natural orifice specimen extraction (NOSE) and to evaluate the short-term efficacy of transcolonic NOSE surgery for resecting specimens of ascending colon cancer. METHODS From January 2016 to May 2017, a retrospective study was conducted in Guangxi. Propensity score matching was used to minimize the bias from nonrandomized treatment assignment. Patients were followed up through May 2020. RESULTS Forty-nine patients underwent totally laparoscopic right hemicolectomy with transcolonic NOSE and 116 patients laparoscopic right hemicolectomy with mini-laparotomy (ML) procedures at our institution. After propensity score matching, each group included 45 patients, and all covariate imbalances were alleviated. The transcolonic NOSE group and the ML group did not differ significantly in terms of baseline clinical characteristics. The transcolonic NOSE group was associated with a shorter time to first flatus (NOSE vs ML: 1.8 ± .5 vs 3.2 ± .8, P = .032), a shorter length of hospital stay (11.3 ± 2.5 days vs 13.0 ± 3.1 days, P = .034), a shorter time to first liquid intake (2.6 ± .8 vs 3.8 ± .9, P = .068), less pain (1.8 ± .8 vs 4.2 ± .7, P = .013), less analgesia requirement (6 [13.3%] vs 21 [46.7%], P = .001), and lower C-reactive protein levels on postoperative day 1 (3.6 ± 1.7 vs 8.2 ± 2.2, P = .001) and postoperative day 3 (NOSE 2.4 ± 1.4 vs M: 4.6 ± 1.7 [P = .013]) than the ML group. The median follow-up was 28.4 months (interquartile range, 18.0-36.0). The 3-year overall survival rates were similar between the transcolonic NOSE group and the ML group. CONCLUSIONS In total, laparoscopic right hemicolectomy with transcolonic specimen extraction appears to be safe for selected patients with ascending colon cancer as a minimally invasive surgery.
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20
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Tanes C, Walker EM, Slisarenko N, Gerrets GL, Grasperge BF, Qin X, Jazwinski SM, Bushman FD, Bittinger K, Rout N. Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection. Viruses 2021; 13:1567. [PMID: 34452432 PMCID: PMC8402875 DOI: 10.3390/v13081567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Gut dysbiosis is a common feature associated with the chronic inflammation of HIV infection. Toward understanding the interplay of chronic treated HIV infection, dysbiosis, and systemic inflammation, we investigated longitudinal fecal microbiome changes and plasma inflammatory markers in the nonhuman primate model. Following simian immunodeficiency virus (SIV) infection in rhesus macaques, significant changes were observed in several members of the phylum Firmicutes along with an increase in Bacteroidetes. Viral suppression with antiretroviral therapy (ART) resulted in an early but partial recovery of compositional changes and butyrate producing genes in the gut microbiome. Over the course of chronic SIV infection and long-term ART, however, the specific loss of Faecalibacterium prausnitzii and Treponema succinifaciens significantly correlated with an increase in plasma inflammatory cytokines including IL-6, G-CSF, I-TAC, and MIG. Further, the loss of T. succinifaciens correlated with an increase in circulating biomarkers of gut epithelial barrier damage (IFABP) and microbial translocation (LBP and sCD14). As F. prausnitzii and T. succinifaciens are major short-chain fatty acid producing bacteria, their sustained loss during chronic SV-ART may contribute to gut inflammation and metabolic alterations despite effective long-term control of viremia. A better understanding of the correlations between the anti-inflammatory bacterial community and healthy gut barrier functions in the setting of long-term ART may have a major impact on the clinical management of inflammatory comorbidities in HIV-infected individuals.
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Affiliation(s)
- Ceylan Tanes
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (C.T.); (K.B.)
| | - Edith M. Walker
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Nadia Slisarenko
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Giovanni L. Gerrets
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Brooke F. Grasperge
- Division of Veterinary Medicine, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA;
| | - Xuebin Qin
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA;
| | - S. Michal Jazwinski
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (C.T.); (K.B.)
| | - Namita Rout
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA;
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21
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Houtz JL, Sanders JG, Denice A, Moeller AH. Predictable and host-species specific humanization of the gut microbiota in captive primates. Mol Ecol 2021; 30:3677-3687. [PMID: 34013536 PMCID: PMC10039810 DOI: 10.1111/mec.15994] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Humans and nonhuman primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts' phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here, we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs' gut microbial clades based on the propensity of their lineages to be lost or replaced in captivity by lineages found in humans. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.
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Affiliation(s)
- Jennifer L. Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anthony Denice
- Project Chimps, Blue Ridge, GA, USA
- Chimpanzee Sanctuary Northwest, Cle Elum, WA, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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22
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Rendina DN, Lubach GR, Lyte M, Phillips GJ, Gosain A, Pierre JF, Vlasova RM, Styner MA, Coe CL. Proteobacteria abundance during nursing predicts physical growth and brain volume at one year of age in young rhesus monkeys. FASEB J 2021; 35:e21682. [PMID: 34042210 DOI: 10.1096/fj.202002162r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 01/01/2023]
Abstract
Over the last decade, multiple studies have highlighted the essential role of gut microbiota in normal infant development. However, the sensitive periods during which gut bacteria are established and become associated with physical growth and maturation of the brain are still poorly defined. This study tracked the assembly of the intestinal microbiota during the initial nursing period, and changes in community structure after transitioning to solid food in infant rhesus monkeys (Macaca mulatta). Anthropometric measures and rectal swabs were obtained at 2-month intervals across the first year of life and bacterial taxa identified by 16S rRNA gene sequencing. At 12 months of age, total brain and cortical regions volumes were quantified through structural magnetic resonance imaging. The bacterial community structure was dynamic and characterized by discrete maturational phases, reflecting an early influence of breast milk and the later transition to solid foods. Commensal microbial taxa varied with diet similar to findings in other animals and human infants; however, monkeys differ in the relative abundances of Lactobacilli and Bifidobacteria, two taxa predominant in breastfed human infants. Higher abundances of taxa in the phylum Proteobacteria during nursing were predictive of slower growth trajectories and smaller brain volumes at one year of age. Our findings define discrete phases of microbial succession in infant monkeys and suggest there may be a critical period during nursing when endogenous differences in certain taxa can shift the community structure and influence the pace of physical growth and the maturational trajectory of the brain.
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Affiliation(s)
- Danielle N Rendina
- Harlow Center, University of Wisconsin, Madison, WI, USA.,Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | | | - Mark Lyte
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Gregory J Phillips
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Ankush Gosain
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Joseph F Pierre
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, USA.,Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Roza M Vlasova
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Martin A Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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23
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Liu Y, Li X, Li J, Chen W. The gut microbiome composition and degradation enzymes activity of black Amur bream ( Megalobrama terminalis) in response to breeding migratory behavior. Ecol Evol 2021; 11:5150-5163. [PMID: 34025998 PMCID: PMC8131771 DOI: 10.1002/ece3.7407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 01/04/2023] Open
Abstract
Black Amur bream (Megalobrama terminalis), a dominant species, resides in the Pearl River basin, known for its high plasticity in digestive ability. During spawning season, M. terminalis individuals with large body size and high fertility undergo a spawn migratory phase, while other smaller individuals prefer to settlement over migration. It is well known that gut microbial community often underpins the metabolic capability and regulates a wide variety of important functions in fish. However, little was known about how the gut microbiomes affect fish breeding migration. To investigate the variations in the gut microbiome of M. terminalis during the migration, we used high-throughput 16S rRNA gene sequencing to reveal the distinct composition and diversity of the whole gut microbiome of migrated and nonmigrated population during period of peak reproduction, respectively. Our results indicated that nonmigrated population in estuary had a higher alpha diversity than that of migrated population in main stem. Additionally, an obvious abundant taxa shift between the gut microbiota community of nonmigrated and migrated M. terminalis was also observed. Change of dominant gut taxa from nonmigrated to migrated population was thought to be closely related to their degradation enzymes. Our results suggested that amino acid metabolism and lipid metabolism in migrated population were higher than that in nonmigrated population, providing a line of evidence for that M. terminalis change from partial herbivorous to partial carnivorous diet during breeding migration. We further concluded that, in order to digest foods of higher nutrition to supply energy to spawning migration, M. terminalis regulate activities of the gut microbiome and degradation enzymes, considered to be a key physiological strategy for reproduction.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
| | - Xinhui Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
| | - Jie Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
| | - Weitao Chen
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
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24
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Compo NR, Mieles-Rodriguez L, Gomez DE. Fecal Bacterial Microbiota of Healthy Free-Ranging, Healthy Corralled, and Chronic Diarrheic Corralled Rhesus Macaques ( Macaca mulatta). Comp Med 2021; 71:152-165. [PMID: 33814032 DOI: 10.30802/aalas-cm-20-000080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A clinical challenge to nearly every primate facility in North America is chronic idiopathic diarrhea (CID), the pathogenesis of which has yet to be fully elucidated. However, wild macaques appear resistant to CID, a trend that we observed in the free-ranging population of the Caribbean Primate Research Center. The gastrointestinal microbiota has been shown to have a significant role in the pathogenesis of disease and in maintaining normal health and development of the gut. In humans, chronic diarrhea is associated with alteration of the gut microbiota, which has lower bacterial diversity than does the microbiota of healthy humans. The current study was designed to describe and compare the fecal bacterial microbiota of healthy corralled, CID corralled, and healthy, free-ranging macaques. Fresh fecal samples were collected from healthy corralled (HC; n = 30) and CID (n = 27) rhesus macaques and from healthy macaques from our free-ranging colony (HF; n = 43). We excluded macaques that had received antibiotics during the preceding 60 d (90 d for healthy animals). Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced and compared with known databases. The relative abundance of Proteobacteria was higher in CID animals than HC animals, but otherwise few differences were found between these 2 groups. HF macaques were differentially enriched with Christensenellaceae and Helicobacter, which are highly associated with a 'healthy' gut in humans, as compared to corralled animals, whereas CID animals were enriched with Proteobacteria, which are associated with dysbiosis in other species. These results indicate that environment has a greater influence than health status on the gut microbiota. Furthermore, the current data provided targets for future studies on potential clinical interventions, such as probiotics and fecal transplants.
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Affiliation(s)
- Nicole R Compo
- Caribbean Primate Research Center, Unit of Comparative Medicine, University of Puerto Rico, Sabana Seca, Puerto Rico; SoBran Bioscience, Norfolk, Virginia;,
| | - Luis Mieles-Rodriguez
- Caribbean Primate Research Center, Unit of Comparative Medicine, University of Puerto Rico, Sabana Seca, Puerto Rico
| | - Diego E Gomez
- Department of Large Animal Clinical Studies, College of Veterinary Medicine, University of Florida, Gainesville, Florida; Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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25
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Klymiuk I, Singer G, Castellani C, Trajanoski S, Obermüller B, Till H. Characterization of the Luminal and Mucosa-Associated Microbiome along the Gastrointestinal Tract: Results from Surgically Treated Preterm Infants and a Murine Model. Nutrients 2021; 13:nu13031030. [PMID: 33806771 PMCID: PMC8004827 DOI: 10.3390/nu13031030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental factors, including nutritional habits or birth mode, are known key determinants for intestinal microbial composition. Investigations of the intestinal microbiome in different species in a multiplicity of studies during recent decades have revealed differential microbial patterns and quantities along the gastrointestinal (GI) tract. Characterization of the microbial pattern in various aspects is a prerequisite for nutritional interventions. In this 16S rRNA amplicon-based approach, we present a characterization of the mucosa-associated microbiome in comparison with the luminal community of four infants at the time of the closure of ileostomies and perform a systematic characterization of the corresponding luminal and mucosal microbiome from jejunal, ileal and colonic regions, as well as collected feces in mice. The most dominant taxa in infant-derived samples altered due to individual differences, and in the mucosa, Enterococcus, Clostridiumsensustricto1, Veillonella, Streptococcus and Staphylococcus were the most abundant. Two less abundant taxa differed significantly between the mucosa and lumen. In murine samples, relative abundances differed significantly, mainly between the intestinal regions. Significant differences between mouse mucosa- and lumen-derived samples could be found in the observed species with a trend to lower estimated diversity in mucosa-derived samples, as well as in the relative abundance of individual taxa. In this study, we examined the difference between the mucosal and luminal bacterial colonization of the gastrointestinal tract in a small sample cohort of preterm infants. Individual differences were characterized and statistical significance was reached in two taxa (Cupriavidus, Ralstonia). The corresponding study on the different murine intestinal regions along the GI tract showed differences all over the intestinal region.
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Affiliation(s)
- Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
- Correspondence: ; Tel.: +43-316-385-83722
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
| | - Slave Trajanoski
- Center for Medical Research, Medical University of Graz, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
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26
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Sokol H, Contreras V, Maisonnasse P, Desmons A, Delache B, Sencio V, Machelart A, Brisebarre A, Humbert L, Deryuter L, Gauliard E, Heumel S, Rainteau D, Dereuddre-Bosquet N, Menu E, Ho Tsong Fang R, Lamaziere A, Brot L, Wahl C, Oeuvray C, Rolhion N, Van Der Werf S, Ferreira S, Le Grand R, Trottein F. SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota. Gut Microbes 2021; 13:1-19. [PMID: 33685349 PMCID: PMC7951961 DOI: 10.1080/19490976.2021.1893113] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The current pandemic of coronavirus disease (COVID) 2019 constitutes a global public health issue. Regarding the emerging importance of the gut-lung axis in viral respiratory infections, analysis of the gut microbiota's composition and functional activity during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection might be instrumental in understanding and controling COVID 19. We used a nonhuman primate model (the macaque), that recapitulates mild COVID-19 symptoms, to analyze the effects of a SARS-CoV-2 infection on dynamic changes of the gut microbiota. 16S rRNA gene profiling and analysis of β diversity indicated significant changes in the composition of the gut microbiota with a peak at 10-13 days post-infection (dpi). Analysis of bacterial abundance correlation networks confirmed disruption of the bacterial community at 10-13 dpi. Some alterations in microbiota persisted after the resolution of the infection until day 26. Some changes in the relative bacterial taxon abundance associated with infectious parameters. Interestingly, the relative abundance of Acinetobacter (Proteobacteria) and some genera of the Ruminococcaceae family (Firmicutes) was positively correlated with the presence of SARS-CoV-2 in the upper respiratory tract. Targeted quantitative metabolomics indicated a drop in short-chain fatty acids (SCFAs) and changes in several bile acids and tryptophan metabolites in infected animals. The relative abundance of several taxa known to be SCFA producers (mostly from the Ruminococcaceae family) was negatively correlated with systemic inflammatory markers while the opposite correlation was seen with several members of the genus Streptococcus. Collectively, SARS-CoV-2 infection in a nonhuman primate is associated with changes in the gut microbiota's composition and functional activity.
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Affiliation(s)
- Harry Sokol
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,INRAE, UMR1319 Micalis & AgroParisTech, Jouy En Josas, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France,CONTACT Harry Sokol Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France
| | - Vanessa Contreras
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - Pauline Maisonnasse
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - Aurore Desmons
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Benoit Delache
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - Valentin Sencio
- Univ. Lille, US 41 - UMS 2014 - PLBS, U1019 - UMR 9017 - CIIL - Centre d’Infection Et d’Immunité De Lille, Lille, France,Centre National De La Recherche Scientifique, Lille, France,Institut National De La Santé Et De La Recherche Médicale U1019, Lille, France,Centre Hospitalier Universitaire De Lille, Lille, France,Institut Pasteur De Lille, Lille, France
| | - Arnaud Machelart
- Univ. Lille, US 41 - UMS 2014 - PLBS, U1019 - UMR 9017 - CIIL - Centre d’Infection Et d’Immunité De Lille, Lille, France,Centre National De La Recherche Scientifique, Lille, France,Institut National De La Santé Et De La Recherche Médicale U1019, Lille, France,Centre Hospitalier Universitaire De Lille, Lille, France,Institut Pasteur De Lille, Lille, France
| | - Angela Brisebarre
- Centre National De Référence Virus Des Infections Respiratoires, Unité De Génétique Moléculaire Des Virus À ARN, GMVR, F75015, Institut Pasteur, UMR CNRS 3569, Université De Paris, Paris, France
| | - Lydie Humbert
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Lucie Deryuter
- Univ. Lille, US 41 - UMS 2014 - PLBS, U1019 - UMR 9017 - CIIL - Centre d’Infection Et d’Immunité De Lille, Lille, France,Centre National De La Recherche Scientifique, Lille, France,Institut National De La Santé Et De La Recherche Médicale U1019, Lille, France,Centre Hospitalier Universitaire De Lille, Lille, France,Institut Pasteur De Lille, Lille, France
| | - Emilie Gauliard
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Severine Heumel
- Univ. Lille, US 41 - UMS 2014 - PLBS, U1019 - UMR 9017 - CIIL - Centre d’Infection Et d’Immunité De Lille, Lille, France,Centre National De La Recherche Scientifique, Lille, France,Institut National De La Santé Et De La Recherche Médicale U1019, Lille, France,Centre Hospitalier Universitaire De Lille, Lille, France,Institut Pasteur De Lille, Lille, France
| | - Dominique Rainteau
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - Elisabeth Menu
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - Raphael Ho Tsong Fang
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - Antonin Lamaziere
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,INRAE, UMR1319 Micalis & AgroParisTech, Jouy En Josas, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Loic Brot
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,INRAE, UMR1319 Micalis & AgroParisTech, Jouy En Josas, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | | | - Cyriane Oeuvray
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Nathalie Rolhion
- Sorbonne Université, INSERM, Centre De Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Sylvie Van Der Werf
- Centre National De Référence Virus Des Infections Respiratoires, Unité De Génétique Moléculaire Des Virus À ARN, GMVR, F75015, Institut Pasteur, UMR CNRS 3569, Université De Paris, Paris, France
| | | | - Roger Le Grand
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (Infectious Diseases Models for Innovative therapies/IDMIT), Paris, France
| | - François Trottein
- Univ. Lille, US 41 - UMS 2014 - PLBS, U1019 - UMR 9017 - CIIL - Centre d’Infection Et d’Immunité De Lille, Lille, France,Centre National De La Recherche Scientifique, Lille, France,Institut National De La Santé Et De La Recherche Médicale U1019, Lille, France,Centre Hospitalier Universitaire De Lille, Lille, France,Institut Pasteur De Lille, Lille, France,François trottein Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, 1 rue du Professeur Calmette, F-59000 Lille, France
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27
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Lee SY, Yuk HG, Ko SG, Cho SG, Moon GS. Gut Microbiome Prolongs an Inhibitory Effect of Korean Red Ginseng on High-Fat-Diet-Induced Mouse Obesity. Nutrients 2021; 13:nu13030926. [PMID: 33809267 PMCID: PMC7999605 DOI: 10.3390/nu13030926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023] Open
Abstract
Although the anti-obesity effect of Korean red ginseng (Panax ginseng Meyer) has been revealed, its underlying mechanisms are not clearly understood. Here, we demonstrate an involvement of gut microbiome in the inhibitory effect of Korean red ginseng on high-fat-diet (HFD)-induced mouse obesity, and further provides information on the effects of saponin-containing red ginseng extract (SGE) and saponin-depleted red ginseng extract (GE). Mice were fed with either SGE or GE every third day for one month, and their food intakes, fat weights, plasma glucose, and insulin and leptin levels were measured. Immunofluorescence assays were conducted to measure pancreatic islet size. Stools from the mice were subjected to metagenomic analysis. Both SGE and GE attenuated HFD-induced gain of body weight, reducing HFD-induced increase of food intakes and fat weights. They also reduced HFD-increased plasma glucose, insulin, and leptin levels, decreased both fasting and postprandial glucose concentrations, and improved both insulin resistance and glucose intolerance. Immunofluorescence assays revealed that they blocked HFD-induced increase of pancreatic islet size. Our pyrosequencing of the 16S rRNA gene V3 region from stools revealed that both SGE and GE modulated HFD-altered composition of gut microbiota. Therefore, we conclude that Korean red ginseng inhibits HFD-induced obesity and diabetes by altering gut microbiome.
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Affiliation(s)
- Seo Yeon Lee
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02453, Korea; (S.Y.L.); (S.G.K.)
| | - Hyun Gyun Yuk
- Department of Food Science and Technology, Korea National University of Transportation, 61 Daehak-ro, Jeungpyeong, Chungbuk 27909, Korea;
| | - Seong Gyu Ko
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02453, Korea; (S.Y.L.); (S.G.K.)
| | - Sung-Gook Cho
- Department of Biotechnology, Korea National University of Transportation, 61 Daehak-ro, Jeungpyeong, Chungbuk 27909, Korea
- Correspondence: (S.-G.C.); (G.-S.M.); Tel.: +82-43-820-5254 (S.-G.C.); +82-43-820-5272 (G.-S.M.)
| | - Gi-Seong Moon
- Department of Biotechnology, Korea National University of Transportation, 61 Daehak-ro, Jeungpyeong, Chungbuk 27909, Korea
- Correspondence: (S.-G.C.); (G.-S.M.); Tel.: +82-43-820-5254 (S.-G.C.); +82-43-820-5272 (G.-S.M.)
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28
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Chen X, Hu B, Huang L, Cheng L, Liu H, Hu J, Hu S, Han C, He H, Kang B, Xu H, Zhang R, Wang J, Li L. The differences in intestinal growth and microorganisms between male and female ducks. Poult Sci 2021; 100:1167-1177. [PMID: 33518075 PMCID: PMC7858134 DOI: 10.1016/j.psj.2020.10.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/03/2020] [Accepted: 10/19/2020] [Indexed: 01/22/2023] Open
Abstract
There are great differences in physiological and biological functions between animals of different sexes. However, whether there is a consensus between sexes in duck intestinal development and microorganisms is still unknown. The current study used Nonghua ducks to estimate the effect of sex on the intestine by evaluating differences in intestinal growth indexes and microorganisms. The intestines of male and female ducks were sampled at 2, 5, and 10 wk from the duodenum, jejunum, ileum, and cecum. Then, the intestinal length and weight were measured, the morphology was observed with HE staining, and the intestinal content was analyzed by 16S rRNA sequencing. The results showed that male ducks have shorter intestinal lengths with higher relative weights/relative lengths. The values of jejunal villus height (VH)/crypt depth (CD) of female ducks were significantly higher at 2 wk, whereas the jejunal VH/CD was significantly lower at 10 wk. There was obvious separation of microorganisms in each intestinal segment of ducks of different sexes at the 3 time periods. The dominant phyla at different stages were Firmicutea, Proteobacteria, Bacteroidetes, and Actinobacteria. The duodenal Chao index at the genus level of male ducks was significantly higher at 10 wk than that of female ducks. Significantly different genera were found only in the jejunum, and the abundances of Escherichia_Shigella, Pseudomonas, Clostridium_sensu_stricto_1, Sphingomonas, and Desulfovibrio in male ducks were higher than those in female ducks, whereas the abundance of Rothia was lower, and the abundance of viral infectious diseases, lipid metabolism, metabolism of terpenoids and polyketides, parasitic infectious diseases, xenobiotic biodegradation and metabolism, cardiovascular disease, and metabolism of other amino acids in male ducks were higher than that in female ducks, whereas gene folding, sorting and degradation pathways, and nucleotide metabolism were lower. This study provides a basic reference for the intestinal development and microbial symbiosis of ducks of different sexes.
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Affiliation(s)
- Xuefei Chen
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Bo Hu
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Liansi Huang
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Lumin Cheng
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Hehe Liu
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Jiwei Hu
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Shenqiang Hu
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Chunchun Han
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Hua He
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Bo Kang
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Hengyong Xu
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Rongping Zhang
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Jiwen Wang
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China
| | - Liang Li
- Work for Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Chengdu, China.
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Prevalence of Vancomycin-Resistant Enterococcus (VRE) in Companion Animals: The First Meta-Analysis and Systematic Review. Antibiotics (Basel) 2021; 10:antibiotics10020138. [PMID: 33572528 PMCID: PMC7911405 DOI: 10.3390/antibiotics10020138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance in companion animals is a major public health concern worldwide due to the animals’ zoonotic potential and ability to act as a reservoir for resistant genes. We report on the first use of meta-analysis and a systematic review to analyze the prevalence of vancomycin-resistant Enterococcus (VRE) in companion animals. Databases such as MedLib, PubMed, Web of Science, Scopus, and Google Scholar were searched. The information was extracted by two independent reviewers and the results were reviewed by a third. Two reviewers independently assessed the study protocol using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist and the study quality using the Joanna Briggs Institute (JBI) critical appraisal checklist for prevalence data. OpenMeta analyst and comprehensive meta-analysis (CMA) were used for the meta-analysis. The random effect model was used, and publication bias was assessed using the Eggers test and funnel plot. Between-study heterogeneity was assessed, and the sources were analyzed using the leave-one-out meta-analysis, subgroup analysis and meta-regression. Twenty-two studies met the eligibility criteria, but because some studies reported the prevalence of VRE in more than one companion animal, they were considered as individual studies, and 35 studies were therefore added to the final meta-analysis. Sampling period of the included studies was from 1995–2018. Of the 4288 isolates tested in the included studies, 1241 were VRE. The pooled prevalence of VRE in companion animals was estimated at 14.6% (95% CI; 8.7–23.5%; I2 = 97.10%; p < 0.001). Between-study variability was high (t2 = 2.859; heterogeneity I2 = 97.10% with heterogeneity chi-square (Q) = 1173.346, degrees of freedom (df) = 34, and p < 0.001). The funnel plot showed bias, which was confirmed by Eggers test (t-value = 3.97165; p = 0.00036), and estimates from the leave-one-out forest plot did not affect the pooled prevalence. Pooled prevalence of VRE in dogs and cats were 18.2% (CI = 9.4–32.5%) and 12.3%, CI = 3.8–33.1%), respectively. More studies were reported in Europe than in any other continent, with most studies using feces as the sample type and disc diffusion as the detection method. With the emergence of resistant strains, new antimicrobials are required in veterinary medicine.
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Warncke G, Singer G, Windhaber J, Schabl L, Friehs E, Miekisch W, Gierschner P, Klymiuk I, Eber E, Zeder K, Pfleger A, Obermüller B, Till H, Castellani C. Volatile Organic Compounds, Bacterial Airway Microbiome, Spirometry and Exercise Performance of Patients after Surgical Repair of Congenital Diaphragmatic Hernia. Molecules 2021; 26:molecules26030645. [PMID: 33530644 PMCID: PMC7865878 DOI: 10.3390/molecules26030645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to analyze the exhaled volatile organic compounds (VOCs) profile, airway microbiome, lung function and exercise performance in congenital diaphragmatic hernia (CDH) patients compared to healthy age and sex-matched controls. A total of nine patients (median age 9 years, range 6-13 years) treated for CDH were included. Exhaled VOCs were measured by GC-MS. Airway microbiome was determined from deep induced sputum by 16S rRNA gene sequencing. Patients underwent conventional spirometry and exhausting bicycle spiroergometry. The exhaled VOC profile showed significantly higher levels of cyclohexane and significantly lower levels of acetone and 2-methylbutane in CDH patients. Microbiome analysis revealed no significant differences for alpha-diversity, beta-diversity and LefSe analysis. CDH patients had significantly lower relative abundances of Pasteurellales and Pasteurellaceae. CDH patients exhibited a significantly reduced Tiffeneau Index. Spiroergometry showed no significant differences. This is the first study to report the VOCs profile and airway microbiome in patients with CDH. Elevations of cyclohexane observed in the CDH group have also been reported in cases of lung cancer and pneumonia. CDH patients had no signs of impaired physical performance capacity, fueling controversial reports in the literature.
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MESH Headings
- Acetone/analysis
- Adolescent
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Child
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Exercise
- Female
- Hernias, Diaphragmatic, Congenital/metabolism
- Hernias, Diaphragmatic, Congenital/physiopathology
- Hernias, Diaphragmatic, Congenital/surgery
- Herniorrhaphy/methods
- Humans
- Male
- Microbiota
- Pentanes/analysis
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Spirometry
- Vital Capacity
- Volatile Organic Compounds/analysis
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Affiliation(s)
- Gert Warncke
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
- Correspondence: ; Tel.: +43-316-385-83722
| | - Jana Windhaber
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Lukas Schabl
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Elena Friehs
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Wolfram Miekisch
- Department of Anesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany; (W.M.); (P.G.)
| | - Peter Gierschner
- Department of Anesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany; (W.M.); (P.G.)
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria;
| | - Ernst Eber
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Katarina Zeder
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Andreas Pfleger
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
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Cardiorespiratory performance capacity and airway microbiome in patients following primary repair of esophageal atresia. Pediatr Res 2021; 90:66-73. [PMID: 33159185 PMCID: PMC8370877 DOI: 10.1038/s41390-020-01222-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/04/2020] [Accepted: 10/11/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Patients following repair of an esophageal atresia (EA) or tracheoesophageal fistula (TEF) carry an increased risk of long-term cardiopulmonary malaise. The role of the airway microbiome in EA/TEF patients remains unclear. METHODS All EA/TEF patients treated between 1980 and 2010 were invited to a prospective clinical examination, spirometry, and spiroergometry. The airway microbiome was determined from deep induced sputum by 16 S rRNA gene sequencing. The results were compared to a healthy age- and sex-matched control group. RESULTS Nineteen EA/TEF patients with a mean age of 24.7 ± 7 years and 19 age- and sex-matched controls were included. EA/TEF patients showed a significantly lower muscle mass, lower maximum vital capacity (VCmax), and higher rates of restrictive ventilation disorders. Spiroergometry revealed a significantly lower relative performance capacity and lower peak VO2 in EA/TEF patients. Alpha- and beta-diversity of the airway microbiome did not differ significantly between the two groups. Linear discriminant effect size analysis revealed significantly enriched species of Prevotella_uncultured, Streptococcus_anginosus, Prevotella_7_Prevotella_enoeca, and Mogibacterium_timidum. CONCLUSION EA/TEF patients frequently suffer from restrictive ventilation disorders and impaired cardiopulmonary function associated with minor alterations of the airway microbiome. Long-term examinations of EA/TEF patients seem to be necessary in order to detect impaired cardiopulmonary function. IMPACT The key messages of the present study are a significantly decreased VCmax and exercise performance, as well as airway microbiome differences in EA/TEF patients. This study is the first to present parameters of lung function and exercise performance in combination with airway microbiome analysis with a mean follow-up of 24 years in EA/TEF patients. Prospective, long-term studies are needed to unravel possible interactions between alterations of the airway microbiome and impaired pulmonary function in EA/TEF patients.
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Kuthyar S, Kowalewski MM, Roellig DM, Mallott EK, Zeng Y, Gillespie TR, Amato KR. Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria. Ecol Evol 2021; 11:45-57. [PMID: 33437414 PMCID: PMC7790644 DOI: 10.1002/ece3.6910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/27/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.
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Affiliation(s)
- Sahana Kuthyar
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
| | - Martin M. Kowalewski
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
- Estación Biológica CorrientesMuseo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN‐CONICET)CorrientesArgentina
| | - Dawn M. Roellig
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention (CDC)AtlantaGAUSA
| | | | - Yan Zeng
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
| | - Thomas R. Gillespie
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
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Firrman J, Liu L, Tanes C, Friedman ES, Bittinger K, Daniel S, van den Abbeele P, Evans B. Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13056-13067. [PMID: 31690071 DOI: 10.1021/acs.jafc.9b05202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The colon gut microbiota is responsible for complex chemical conversions of nutrients and subsequent release of metabolites that have diverse biological consequences. However, information on the metabolic dynamics that occur longitudinally through the colon is limited. Here, gas and liquid chromatographies coupled with mass spectrometry were applied to generate metabolic profiles of the region-specific microbial communities cultured using an in vitro platform simulating the ascending (AC), transverse (TC), and descending (DC) colon regions. Comparative analysis revealed a large divergence between metabolic profiles of the AC and the TC and DC regions in terms of short-chain fatty acid production, metabolic spectrum, and conversion of bile acids. Metagenomic evaluation revealed that the regionally derived metabolic profiles had strong correlation to community composition and genetic potential. Together, the results provide key insights regarding the metabolic divergence of the regional communities that are integral to understand the structure-function relationship of the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wyndmoor, Pennsylvania 19038, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wyndmoor, Pennsylvania 19038, United States
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Elliot S Friedman
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | | | - Bradley Evans
- Proteomics & Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, Missouri 63132, United States
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Lang S, Fairfied B, Gao B, Duan Y, Zhang X, Fouts DE, Schnabl B. Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients. Gut Microbes 2020; 12:1785251. [PMID: 32684075 PMCID: PMC7524371 DOI: 10.1080/19490976.2020.1785251] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND AND AIMS Alcoholic hepatitis is the most severe form of alcohol-related liver disease. While the gut microbiome is known to play a role in disease development and progression, less is known about specific compositional changes of the gut bacterial microbiome associated with disease severity. Therefore, the aim of our study was to correlate gut microbiota features with disease severity in alcoholic hepatitis patients. METHODS We used 16S rRNA gene sequencing on fecal samples from 74 alcoholic hepatitis patients, which were enrolled at 9 centers in Europe, the United States, and Mexico in a multi-center observational study. The relative abundance of gut bacterial taxa on genus level, as well as the microbiome diversity, was correlated to various clinical, laboratory, and histologic parameters. RESULTS We observed a negative correlation between the model for end-stage liver disease score and Shannon diversity, independent of potentially confounding factors (Padjust = 0.046). Alcoholic hepatitis patients with more severe disease had significantly decreased relative abundances of Akkermansia while the relative abundance of Veillonella was increased. We observed a reduction in the Bacteroides abundance (Padjust = 0.048) and Shannon diversity (Padjust = 0.018) in antibiotic-treated patients and patients receiving steroids had an increase in Veillonella abundance (Padjust = 0.005), which was both independent of potentially confounding factors. CONCLUSION We observed distinct changes in the gut bacterial microbiome of alcoholic hepatitis patients with more severe disease. The gut bacterial microbiome might be an attractive target to prevent and treat this deadly disease.
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Affiliation(s)
- Sonja Lang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bradley Fairfied
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bei Gao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Derrick E. Fouts
- J.Craig Venter Institute, Department for Genomic Medicine, Rockville, MD, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA,CONTACT Bernd Schnabl Department of Medicine, University of California San Diego, La Jolla, CA92093, USA
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Han M, Yang K, Yang P, Zhong C, Chen C, Wang S, Lu Q, Ning K. Stratification of athletes' gut microbiota: the multifaceted hubs associated with dietary factors, physical characteristics and performance. Gut Microbes 2020; 12:1-18. [PMID: 33289609 PMCID: PMC7734118 DOI: 10.1080/19490976.2020.1842991] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gut microbial communities of athletes differ from that of sedentary persons in both diversity and the presence of certain taxa. However, it is unclear to what degree elite athletes and non-elite athletes harbor different gut microbial community patterns and if we can effectively monitor the potential of athletes based on microbiota. A team of professional female rowing athletes in China was recruited and 306 fecal samples were collected from 19 individuals, which were separated into three cohorts: adult elite athlete's (AE), youth elite athlete's (YE), and youth non-elite athlete's (YN). The differences in gut microbiome among different cohorts were compared, and their associations with dietary factors, physical characteristics, and athletic performance were investigated. The microbial diversities of elite athletes were higher than those of youth non-elite athletes. The taxonomical, functional, and phenotypic compositions of AE, YE and YN were significantly different. Additionally, three enterotypes with clear separation were identified in athlete's fecal samples, with majority of elite athletes stratified into enterotype 3. And this enterotype-dependent gut microbiome is strongly associated with athlete performances. These differences in athlete gut microbiota lead to establishment of a random forest classifier based on taxonomical and functional biomarkers, capable of differentiating elite athletes and non-elite athletes with high accuracy. Finally, these versatilities of athlete microbial communities of athletes were found to be associated with dietary factors and physical characteristics, which can in concert explain 41% of the variability in gut microbiome.
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Affiliation(s)
- Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China,CONTACT Kang Ning
| | - Kun Yang
- Exercise Immunology Center, Wuhan Sports University, Wuhan, Hubei, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Song Wang
- Exercise Immunology Center, Wuhan Sports University, Wuhan, Hubei, China,Song Wang Exercise Immunology Center, Wuhan Sports University, Wuhan, Hubei430079, China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,Qunwei Lu Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,CONTACT Kang Ning
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Siddiqui S, Bao D, Doyle-Meyers L, Dufour J, Wu Y, Liu YZ, Ling B. Alterations of the gut bacterial microbiota in rhesus macaques with SIV infection and on short- or long-term antiretroviral therapy. Sci Rep 2020; 10:19056. [PMID: 33149234 PMCID: PMC7642356 DOI: 10.1038/s41598-020-76145-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
Gut dysbiosis and microbial translocation are associated with chronic systemic immune activation and inflammation in HIV-1 infection. However, the extent of restoration of gut microbiota in HIV-1 patients with short or long-term antiretroviral therapy (ART) is unclear. To understand the impact of ART on the gut microbiota, we used the rhesus macaque model of SIV infection to characterize and compare the gut microbial community upon SIV infection and during ART. We observed altered taxonomic compositions of gut microbiota communities upon SIV infection and at different time points of ART. SIV-infected animals showed decreased diversity of gut microbiome composition, while the ART group appeared to recover towards the diversity level of the healthy control. Animals undergoing ART for various lengths of time were observed to have differential gut bacterial abundance across different time points. In addition, increased blood lipopolysaccharide (LPS) levels during SIV infection were reduced to near normal upon ART, indicating that microbial translocation and immune activation can be improved during therapy. In conclusion, while short ART may be related to transient increase of certain pathogenic bacterial microbiome, ART may promote microbiome diversity compromised by SIV infection, improve the gut microbiota towards the healthy compositions and alleviate immune activation.
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Affiliation(s)
- Summer Siddiqui
- Tulane National Primate Research Center, Covington, LA, 70433, USA
| | - Duran Bao
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | | | - Jason Dufour
- Tulane National Primate Research Center, Covington, LA, 70433, USA
| | - Yuntao Wu
- Department of Molecular and Microbiology, National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Yao-Zhong Liu
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Binhua Ling
- Tulane National Primate Research Center, Covington, LA, 70433, USA. .,Tulane Center for Aging, School of Medicine, Tulane University, New Orleans, LA, 70112, USA. .,Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA, 70112, USA. .,Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX, 78227, USA.
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Liu J, Huang S, Li G, Zhao J, Lu W, Zhang Z. High housing density increases stress hormone- or disease-associated fecal microbiota in male Brandt's voles (Lasiopodomys brandtii). Horm Behav 2020; 126:104838. [PMID: 32791065 DOI: 10.1016/j.yhbeh.2020.104838] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/31/2022]
Abstract
Density-dependence is an important mechanism in the population regulation of small mammals. Stressors induced by high-density (e.g., crowding and aggression) can cause physiological and neurological disorders, and are hypothesized to be associated with alterations in gut microbiota, which may in turn reduce the fitness of animals by increasing stress- or disease-associated microbes. In this study, we examined the effects of housing density on the hormone levels, immunity, and composition of gut microbiota in male Brandt's voles (Lasiopodomys brandtii) by conducting two specific housing density experiments with or without physical contact between voles. Voles in high density groups exhibited higher serum corticosterone (CORT), serotonin (5-HT), and immunoglobulin G (IgG) levels, as well as higher testosterone (T) levels only in the experiment with physical contact. Meanwhile, high-density treatments induced significant changes in the composition of gut microbiota by increasing disease-associated microbes. The levels of hormones and immunity (i.e., CORT, 5-HT, and IgG) elevated by the high density treatment were significantly correlated with some specific microbes. These results imply that high-density-induced stress may shape the fitness of animals under natural conditions by altering their gut microbiota. Our study provides novel insights into the potential roles of gut microbiota in the density-dependent population regulation of small rodents as well as the potential mechanisms underlying psychological disorders in humans and animals under crowded conditions.
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Affiliation(s)
- Jing Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuli Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jidong Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhu C, Xu W, Tao Z, Song W, Liu H, Zhang S, Li H. Effects of Rearing Conditions and Sex on Cecal Microbiota in Ducks. Front Microbiol 2020; 11:565367. [PMID: 33133040 PMCID: PMC7578374 DOI: 10.3389/fmicb.2020.565367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/10/2020] [Indexed: 01/14/2023] Open
Abstract
The intestinal microbiome influences the health of animals. However, little is known about the impact of indoor conditions and sex on intestinal microbiome diversity and composition in ducks. The present study aimed to investigate differences in the cecal microbiome between male and female ducks reared on the floor (PY group) or in cages (LY group). We also determined the relationships between cecal microbiota composition and slaughter traits, and the expression levels of mucosal and intestinal structural genes in ducks. There was a slight difference in slaughter traits among the groups, with cecum weight being significantly lighter in the LY compared with the PY group, especially in females (p < 0.05). Analysis of the alpha diversity of the cecal microbiota between males and females in the LY and PY groups showed that LY males had significantly lower diversity and richness. Beta diversity analysis demonstrated differences in the microbiota composition in relation to rearing conditions, and a significant difference between the sexes in the PY groups. The dominant bacterial phyla in duck cecum were Bacteroidetes, Firmicutes, Proteobacteria, and Fusobacteria. The relative abundances of the most common bacteria revealed that the intestinal microbiota diversity and composition were affected by both feeding conditions and sex. Several bacterial genera were detected differentially among the groups. These genera were correlated with slaughter traits and expression levels of mucosal and cecal structural genes in ducks. In conclusion, rearing conditions, sex, and associated changes in the cecal microbiota are thus associated with gut barrier functions in ducks.
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Affiliation(s)
- Chunhong Zhu
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Wenjuan Xu
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Zhiyun Tao
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Hongxiang Liu
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | | | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
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Om K, Paquin-Proulx D, Montero M, Peachman K, Shen X, Wieczorek L, Beck Z, Weiner JA, Kim D, Li Y, Mdluli T, Shubin Z, Bryant C, Sharma V, Tokarev A, Dawson P, White Y, Appelbe O, Klatt NR, Tovanabutra S, Estes JD, Matyas GR, Ferrari G, Alving CR, Tomaras GD, Ackerman ME, Michael NL, Robb ML, Polonis V, Rolland M, Eller MA, Rao M, Bolton DL. Adjuvanted HIV-1 vaccine promotes antibody-dependent phagocytic responses and protects against heterologous SHIV challenge. PLoS Pathog 2020; 16:e1008764. [PMID: 32881968 PMCID: PMC7505435 DOI: 10.1371/journal.ppat.1008764] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/21/2020] [Accepted: 06/30/2020] [Indexed: 01/29/2023] Open
Abstract
To augment HIV-1 pox-protein vaccine immunogenicity using a next generation adjuvant, a prime-boost strategy of recombinant modified vaccinia virus Ankara and multimeric Env gp145 was evaluated in macaques with either aluminum (alum) or a novel liposomal monophosphoryl lipid A (MPLA) formulation adsorbed to alum, ALFA. Binding antibody responses were robust and comparable between arms, while antibody-dependent neutrophil and monocyte phagocytotic responses were greatly enhanced by ALFA. Per-exposure vaccine efficacy against heterologous tier 2 SHIV mucosal challenge was 90% in ALFA-adjuvanted males (P = 0.002), while alum conferred no protection. Half of the ALFA-adjuvanted males remained uninfected after the full challenge series, which spanned seven months after the last vaccination. Antibody-dependent monocyte and neutrophil phagocytic responses both strongly correlated with protection. Significant sex differences in infection risk were observed, with much lower infection rates in females than males. In humans, MPLA-liposome-alum adjuvanted gp120 also increased HIV-1-specific phagocytic responses relative to alum. Thus, next-generation liposome-based adjuvants can drive vaccine elicited antibody effector activity towards potent phagocytic responses in both macaques and humans and these responses correlate with protection. Future protein vaccination strategies aiming to improve functional humoral responses may benefit from such adjuvants.
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Affiliation(s)
- Kier Om
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Dominic Paquin-Proulx
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Maria Montero
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kristina Peachman
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Lindsay Wieczorek
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Zoltan Beck
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Joshua A. Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Dohoon Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Yifan Li
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Thembi Mdluli
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Zhanna Shubin
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | | | - Vishakha Sharma
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Peter Dawson
- EMMES, Rockville, Maryland, United States of America
| | - Yohann White
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Oliver Appelbe
- Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America
| | - Nichole R. Klatt
- Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Jacob D. Estes
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
| | - Gary R. Matyas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Carl R. Alving
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Victoria Polonis
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Michael A. Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Mangala Rao
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
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Shanmuganandam S, Hu Y, Strive T, Schwessinger B, Hall RN. Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia. PeerJ 2020; 8:e9564. [PMID: 32874776 PMCID: PMC7441920 DOI: 10.7717/peerj.9564] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/26/2020] [Indexed: 12/31/2022] Open
Abstract
Background European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. Methods We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms. Results We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.
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Affiliation(s)
- Somasundhari Shanmuganandam
- Research School of Biology, Australian National University, Acton, ACT, Australia.,Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Yiheng Hu
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Tanja Strive
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Centre for Invasive Species Solutions, Bruce, ACT, Australia
| | | | - Robyn N Hall
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Centre for Invasive Species Solutions, Bruce, ACT, Australia
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41
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Allers K, Stahl-Hennig C, Fiedler T, Wibberg D, Hofmann J, Kunkel D, Moos V, Kreikemeyer B, Kalinowski J, Schneider T. The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4 + T cell depletion and enterocyte damage. Sci Rep 2020; 10:10887. [PMID: 32616803 PMCID: PMC7331662 DOI: 10.1038/s41598-020-67843-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/08/2020] [Indexed: 01/01/2023] Open
Abstract
The intesinal microbiome is considered important in human immunodeficiency virus (HIV) pathogenesis and therefore represents a potential therapeutic target to improve the patients’ health status. Longitudinal alterations in the colonic mucosa-associated microbiome during simian immunodeficiency virus (SIV) infection were investigated using a 16S rRNA amplicon approach on the Illumina sequencing platform and bioinformatics analyses. Following SIV infection of six animals, no alterations in microbial composition were observed before the viral load peaked in the colon. At the time of acute mucosal SIV replication, the phylum Bacteroidetes including the Bacteroidia class as well as the phylum Firmicutes and its families Ruminococcaceae and Eubacteriaceae became more abundant. Enrichment of Bacteroidetes was maintained until the chronic phase of SIV infection. The shift towards Bacteroidetes in the mucosa-associated microbiome was associated with the extent of SIV infection-induced mucosal CD4+ T cell depletion and correlated with increasing rates of enterocyte damage. These observations suggest that Bacteroidetes strains increase during virus-induced mucosal immune destruction. As Bacteroidetes belong to the lipopolysaccharide- and short chain fatty acids-producing bacteria, their rapid enrichment may contribute to inflammatory tissue damage and metabolic alterations in SIV/HIV infection. These aspects should be considered in future studies on therapeutic interventions.
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Affiliation(s)
- Kristina Allers
- Department of Gastroenterology, Infectious Diseases, and Rheumatology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203, Berlin, Germany.
| | | | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, 18057, Rostock, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615, Bielefeld, Germany
| | - Jörg Hofmann
- Institute of Medical Virology, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117, Berlin, Germany
| | - Désirée Kunkel
- Department of Gastroenterology, Infectious Diseases, and Rheumatology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, 13353, Berlin, Germany
| | - Verena Moos
- Department of Gastroenterology, Infectious Diseases, and Rheumatology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, 18057, Rostock, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615, Bielefeld, Germany
| | - Thomas Schneider
- Institute of Medical Virology, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117, Berlin, Germany
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Sun DL, Gao YZ, Ge XY, Shi ZL, Zhou NY. Special Features of Bat Microbiota Differ From Those of Terrestrial Mammals. Front Microbiol 2020; 11:1040. [PMID: 32582057 PMCID: PMC7284282 DOI: 10.3389/fmicb.2020.01040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Bats (order Chiroptera) are one of the most diverse and widely distributed group of mammals with a close relationship to humans. Over the past few decades, a number of studies have been performed on bat viruses; in contrast, bacterial pathogens carried by bats were largely neglected. As more bacterial pathogens are being identified from bats, the need to study their natural microbiota is becoming urgent. In the current study, fecal samples of four bat species from different locations of China were analyzed for their microbiota composition. Together with the results of others, we concluded that bat microbiota is most commonly dominated by Firmicutes and Proteobacteria; the strict anaerobic phylum Bacteroidetes, which is dominant in other terrestrial mammals, especially humans and mice, is relatively rare in bats. This phenomenon was interpreted as a result of a highly specified gastrointestinal tract in adaptation to the flying lifestyle of bats. Further comparative study implied that bat microbiota resemble those of the order Carnivora. To discover potential bacterial pathogens, a database was generated containing the 16S rRNA gene sequences of known bacterial pathogens. Potential bacterial pathogens belonging to 12 genera were detected such as Salmonella, Shigella, and Yersinia, among which some have been previously reported in bats. This study demonstrated high resolution and repeatability in detecting organisms of rare existence, and the results could be used as guidance for future bacterial pathogen isolation.
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Affiliation(s)
- Dong-Lei Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Zhou Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Yi Ge
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,College of Biology, Hunan University, Changsha, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ning-Yi Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Zollner-Schwetz I, Scarpatetti M, Pichler G, Pux C, Klymiuk I, Trajanoski S, Krause R. Effect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study. Nutrients 2020; 12:nu12061586. [PMID: 32481668 PMCID: PMC7352861 DOI: 10.3390/nu12061586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 01/02/2023] Open
Abstract
Residents in long-term care facilities (LTCFs) are frequently colonized by multidrug-resistant Gram-negative bacteria, putting them at risk for subsequent infections. We aimed to evaluate the effect of the multispecies probiotic Omnibiotic10AAD® on the intestinal and inguinal skin colonization of patients by multidrug-resistant Gram-negative bacteria in LTCFs. Patients colonized by multidrug-resistant Gram-negative bacteria received a 12 week oral course of Omnibiotic10AAD®. Inguinal swabs and stool samples were collected during and after treatment for microbiological and microbiome analysis. The median age of patients was 76 years. Twelve patients completed the pilot study. Intestinal colonization was reduced to 42% of patients 8 weeks after the end of treatment, but increased to 66% 24 weeks after the end of probiotic treatment. Colonization of inguinal skin was lowest during probiotic treatment and increased thereafter. Fecal microbiome analysis revealed statistically significant increases of the genus Enterococcus comparing start and end of probiotic treatment. In conclusion, a 12 week course of a multispecies probiotic led to a transient reduction of intestinal colonization 8 weeks after the end of treatment. The findings of our pilot study warrant further research in the area of probiotics and intestinal colonization by multidrug-resistant bacteria.
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Affiliation(s)
- Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
- Correspondence:
| | - Monika Scarpatetti
- Geriatric Health Centres of the City of Graz, Albert-Schweitzer-Gasse 36, 8020 Graz, Austria; (M.S.); (G.P.); (C.P.)
| | - Gerald Pichler
- Geriatric Health Centres of the City of Graz, Albert-Schweitzer-Gasse 36, 8020 Graz, Austria; (M.S.); (G.P.); (C.P.)
| | - Christian Pux
- Geriatric Health Centres of the City of Graz, Albert-Schweitzer-Gasse 36, 8020 Graz, Austria; (M.S.); (G.P.); (C.P.)
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Centre for Medical Research, Medical University of Graz, Stiftingtalstraße 24/1, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Slave Trajanoski
- Core Facility Molecular Biology, Centre for Medical Research, Medical University of Graz, Stiftingtalstraße 24/1, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
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Abstract
In a healthy colon, the microbiota produces a vast amount of metabolites that are essential to maintaining homeostasis in the colon microenvironment. In fact, these metabolites produced by the microbiota have been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. In this study, we used healthy nonhuman primate models to investigate the relationship between microbiota and tissue metabolites. We found that both microbiota and metabolites have location-specific signatures along the intestine. Most importantly, we found that metabolites from food sources correlate with multiple bacteria in different intestinal locations. Overall, this work presents a systems-level map of the association between the microbiota and the metabolites in healthy nonhuman primates, provides candidates for experimental validation, and suggests a possibility to regulate the gut microbiota through specific prebiotic combinations. The intestinal microbiota is highly metabolically active and plays an important role in many metabolic processes absent from the human host. Altered microbiota metabolism has been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. However, there is a gap in the current knowledge on how the microbiota interact with its host in terms of metabolic interactions. Here, we performed an integrated analysis between the mucosa-associated microbiota and the mucosa metabolome in healthy, nonhuman primates to investigate these relationships. The microbiota composition was distinct at each tissue location, with variation by host individual also observed. Microbiota-metabolome dynamics were primarily driven by interactions in the distal colon. These interactions were strongly correlated with dietary component, indicating a possibility to modulate microbiota-metabolomic interactions using prebiotic strategies. IMPORTANCE In a healthy colon, the microbiota produces a vast amount of metabolites that are essential to maintaining homeostasis in the colon microenvironment. In fact, these metabolites produced by the microbiota have been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. In this study, we used healthy nonhuman primate models to investigate the relationship between microbiota and tissue metabolites. We found that both microbiota and metabolites have location-specific signatures along the intestine. Most importantly, we found that metabolites from food sources correlate with multiple bacteria in different intestinal locations. Overall, this work presents a systems-level map of the association between the microbiota and the metabolites in healthy nonhuman primates, provides candidates for experimental validation, and suggests a possibility to regulate the gut microbiota through specific prebiotic combinations.
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45
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Rubel MA, Abbas A, Taylor LJ, Connell A, Tanes C, Bittinger K, Ndze VN, Fonsah JY, Ngwang E, Essiane A, Fokunang C, Njamnshi AK, Bushman FD, Tishkoff SA. Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. Genome Biol 2020; 21:122. [PMID: 32450885 PMCID: PMC7249393 DOI: 10.1186/s13059-020-02020-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia. RESULTS We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids. CONCLUSIONS These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.
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Affiliation(s)
- Meagan A. Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Present Address: Department of Radiology, Center for Translational Imaging and Precision Medicine, UC San Diego, San Diego, CA USA
| | - Arwa Abbas
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Present Address: Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Louis J. Taylor
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Andrew Connell
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Valantine N. Ndze
- Johns Hopkins Cameroon Program, Yaoundé, Cameroon
- Department of Microbiology, Hematology, Parasitology and Infectious Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Julius Y. Fonsah
- Department of Neurology, Faculty of Medicine and Biomedical Sciences, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Eric Ngwang
- Department of Anthropology, Faculty of Arts, Letters and Social Sciences, University of Yaoundé I, PO Box 755, Yaoundé, Cameroon
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sarah A. Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
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Ji J, Xu Y, Luo C, He Y, Xu X, Yan X, Li Y, Shu D, Qu H. Effects of the DMRT1 genotype on the body weight and gut microbiota in the broiler chicken. Poult Sci 2020; 99:4044-4051. [PMID: 32731992 PMCID: PMC7597928 DOI: 10.1016/j.psj.2020.03.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/02/2020] [Accepted: 03/23/2020] [Indexed: 11/30/2022] Open
Abstract
Intestinal microbiota is a critical determinant of growth and risk of metabolic diseases. Our previous studies showed that the locus rs16775833 within the DMRT1 gene is significantly associated with variation in the population structure of the gut microbiota, which is involved in determining the BW of the chicken. To assess the accuracy of correlation of rs16775833 located in the DMRT1 gene on microbial population and BW in birds, 2 genotypes GG and TT in the rs16775833 were identified in Chinese Yellow broiler breeders. We found that BW in the TT genotype group was significantly higher than in the GG genotype group at 7 and 13 wk of age in 777 female chickens. A full-length 16S rRNA sequencing approach was used to further evaluate the fecal bacterial composition of female broilers in 11 TT genotype chickens with high weight (HW-TT) and 11 GG genotype chickens with low weight (LW-GG) at 91 D of age. Partial least squares discriminant analysis revealed that the microbiota of the HW-TT and LW-GG females were clearly separated into 2 clusters. Furthermore, we identified 13 significantly different (P < 0.05) microbes at the genus level and 17 significantly different (P < 0.05) species between the HW-TT and LW-GG groups. Our data show that rs16775833 can modulate the microbial community structure and is associated with the BW of birds. To our knowledge, this is the first time that DMRT1 has been identified as a specific host factor, which is not only involved in sex determination but also has an effect on microbial function that might regulate animal growth.
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Affiliation(s)
- Jian Ji
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yibin Xu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yanhua He
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xinchun Xu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xia Yan
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Ying Li
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
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Blum FC, Hardy BL, Bishop-Lilly KA, Frey KG, Hamilton T, Whitney JB, Lewis MG, Merrell DS, Mattapallil JJ. Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy. Sci Rep 2020; 10:6387. [PMID: 32286417 PMCID: PMC7156522 DOI: 10.1038/s41598-020-63196-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/07/2020] [Indexed: 02/08/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection is characterized by a massive loss of CD4 T cells in the gastrointestinal tract (GIT) that is accompanied by changes in the gut microbiome and microbial translocation that contribute to inflammation and chronic immune activation. Though highly active antiretroviral therapy (HAART) has led to better long-term outcomes in HIV infected patients, it has not been as effective at reverting pathogenesis in the GIT. Using the simian immunodeficiency virus (SIV) infection model, we show that combination antiretroviral therapy (c-ART) partially reverted microbial dysbiosis observed during SIV infection. Though the relative abundance of bacteria, their richness or diversity did not significantly differ between infected and treated animals, microbial dysbiosis was evident via multiple beta diversity metrics: Jaccard similarity coefficient, Bray-Curtis similarity coefficient, and Yue & Clayton theta similarity coefficient. Principal coordinates analysis (PCoA) clustered SIV-infected untreated animals away from healthy and treated animals that were clustered closely, indicating that c-ART partially reversed the gut dysbiosis associated with SIV infection. Metastats analysis identified specific operational taxonomic units (OTUs) falling within the Streptococcus, Prevotella, Acinetobacter, Treponema, and Lactobacillus genera that were differentially represented across the three groups. Our results suggest that complete viral suppression with c-ART could potentially revert microbial dysbiosis observed during SIV and HIV infections.
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Affiliation(s)
- Faith C Blum
- F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States
| | - Britney L Hardy
- F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States
| | - Kimberly A Bishop-Lilly
- Genomics & Bioinformatics Department, Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Kenneth G Frey
- Genomics & Bioinformatics Department, Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Theron Hamilton
- Genomics & Bioinformatics Department, Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | | | - D Scott Merrell
- F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States.
| | - Joseph J Mattapallil
- F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States.
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48
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Vujkovic-Cvijin I, Somsouk M. HIV and the Gut Microbiota: Composition, Consequences, and Avenues for Amelioration. Curr HIV/AIDS Rep 2020; 16:204-213. [PMID: 31037552 DOI: 10.1007/s11904-019-00441-w] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We discuss recent advances in understanding of gut bacterial microbiota composition in HIV-infected subjects and comment on controversies. We discuss the putative effects of microbiota shifts on systemic inflammation and HIV disease progression and potential mechanisms, as well as ongoing strategies being developed to modulate the gut microbiota in humans for amelioration of infectious and inflammatory diseases. RECENT FINDINGS Lifestyle and behavioral factors relevant to HIV infection studies have independent effects on the microbiota. Microbial metabolism of immunomodulatory compounds and direct immune stimulation by translocation of microbes are putative mechanisms contributing to HIV disease. Fecal microbiota transplantation, microbial enzyme inhibition, phage therapy, and rationally selected probiotic cocktails have emerged as promising strategies for microbiota modulation. Numerous surveys of the HIV gut microbiota matched for lifestyle factors suggest consistent shifts in gut microbiota composition among HIV-infected subjects. Evidence exists for a complex pathogenic role of the gut microbiota in HIV disease progression, warranting further study.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, National Institute of Allergy & Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, CA, USA.
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49
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Murray MH, Lankau EW, Kidd AD, Welch CN, Ellison T, Adams HC, Lipp EK, Hernandez SM. Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird. PLoS One 2020; 15:e0220926. [PMID: 32134945 PMCID: PMC7058277 DOI: 10.1371/journal.pone.0220926] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial communities in the gastrointestinal tract influence many aspects of host health, including metabolism and susceptibility to pathogen colonization. These relationships and the environmental and individual factors that drive them are relatively unexplored for free-living wildlife. We quantified the relationships between urban habitat use, diet, and age with microbiome composition and diversity for 82 American white ibises (Eudocimus albus) captured along an urban gradient in south Florida and tested whether gut microbial diversity was associated with Salmonella enterica prevalence. Shifts in community composition were significantly associated with urban land cover and, to a lesser extent, diets higher in provisioned food. The diversity of genera was negatively associated with community composition associated with urban land cover, positively associated with age class, and negatively associated with Salmonella shedding. Our results suggest that shifts in both habitat use and diet for urban birds significantly alter gut microbial composition and diversity in ways that may influence health and pathogen susceptibility as species adapt to urban habitats.
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Affiliation(s)
- Maureen H. Murray
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
| | - Emily W. Lankau
- University of Wisconsin Department of Animal Sciences, Madison, Wisconsin, United States of America
- Ronin Institute, Montclair, New Jersey, United States of America
| | - Anjelika D. Kidd
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
| | - Catharine N. Welch
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Taylor Ellison
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Henry C. Adams
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Sonia M. Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
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50
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Han Q, Bradley T, Williams WB, Cain DW, Montefiori DC, Saunders KO, Parks RJ, Edwards RW, Ferrari G, Mueller O, Shen X, Wiehe KJ, Reed S, Fox CB, Rountree W, Vandergrift NA, Wang Y, Sutherland LL, Santra S, Moody MA, Permar SR, Tomaras GD, Lewis MG, Van Rompay KKA, Haynes BF. Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization. Cell Rep 2020; 30:1553-1569.e6. [PMID: 32023469 PMCID: PMC7243677 DOI: 10.1016/j.celrep.2019.12.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/16/2019] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
HIV-1-infected infants develop broadly neutralizing antibodies (bnAbs) more rapidly than adults, suggesting differences in the neonatal versus adult responses to the HIV-1 envelope (Env). Here, trimeric forms of HIV-1 Env immunogens elicit increased gp120- and gp41-specific antibodies more rapidly in neonatal macaques than adult macaques. Transcriptome analyses of neonatal versus adult immune cells after Env vaccination reveal that neonatal macaques have higher levels of the apoptosis regulator BCL2 in T cells and lower levels of the immunosuppressive interleukin-10 (IL-10) receptor alpha (IL10RA) mRNA transcripts in T cells, B cells, natural killer (NK) cells, and monocytes. In addition, immunized neonatal macaques exhibit increased frequencies of activated blood T follicular helper-like (Tfh) cells compared to adults. Thus, neonatal macaques have transcriptome signatures of decreased immunosuppression and apoptosis compared with adult macaques, providing an immune landscape conducive to early-life immunization prior to sexual debut.
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Affiliation(s)
- Qifeng Han
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert J Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Regina W Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Olaf Mueller
- Center for Genomics of Microbial Systems, Duke University Medical Center, Durham, NC, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin J Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sallie R Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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