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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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Svobodová K, Maitre A, Obregón D, Wu-Chuang A, Thaduri S, Locke B, de Miranda JR, Mateos-Hernández L, Krejčí AB, Cabezas-Cruz A. Gut microbiota assembly of Gotland varroa-surviving honey bees excludes major viral pathogens. Microbiol Res 2023; 274:127418. [PMID: 37315341 DOI: 10.1016/j.micres.2023.127418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023]
Abstract
The spread of the parasite Varroa destructor and associated viruses has resulted in massive honey bee colony losses with considerable economic and ecological impact. The gut microbiota has a major role in shaping honey bees tolerance and resistance to parasite infestation and viral infection, but the contribution of viruses to the assembly of the host microbiota in the context of varroa resistance and susceptibility remains unclear. Here, we used a network approach including viral and bacterial nodes to characterize the impact of five viruses, Apis Rhabdovirus-1 (ARV-1), Black Queen Cell virus (BQCV), Lake Sinai virus (LSV), Sacbrood virus (SBV) and Deformed wing virus (DWV) on the gut microbiota assembly of varroa-susceptible and Gotland varroa-surviving honey bees. We found that microbiota assembly was different in varroa-surviving and varroa-susceptible honey bees with the network of the latter having a whole module not present in the network of the former. Four viruses, ARV-1, BQCV, LSV, and SBV, were tightly associated with bacterial nodes of the core microbiota of varroa-susceptible honey bees, while only two viruses BQCV and LSV, appeared correlated with bacterial nodes in varroa-surviving honey bees. In silico removal of viral nodes caused major re-arrangement of microbial networks with changes in nodes centrality and significant reduction of the networks' robustness in varroa-susceptible, but not in varroa-surviving honey bees. Comparison of predicted functional pathways in bacterial communities using PICRUSt2 showed the superpathway for heme b biosynthesis from uroporphyrinogen-III and a pathway for arginine, proline, and ornithine interconversion as significantly increased in varroa-surviving honey bees. Notably, heme and its reduction products biliverdin and bilirubin have been reported as antiviral agents. These findings show that viral pathogens are differentially nested in the bacterial communities of varroa-surviving and varroa-susceptible honey bees. These results suggest that Gotland honey bees are associated with minimally-assembled and reduced bacterial communities that exclude viral pathogens and are resilient to viral nodes removal, which, together with the production of antiviral compounds, may explain the resiliency of Gotland honey bees to viral infections. In contrast, the intertwined virus-bacterium interactions in varroa-susceptible networks suggest that the complex assembly of microbial communities in this honey bee strain favor viral infections, which may explain viral persistence in this honey bee strain. Further understanding of protective mechanisms mediated by the microbiota could help developing novel ways to control devastating viral infections affecting honey bees worldwide.
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Affiliation(s)
- Karolína Svobodová
- University of South Bohemia, Faculty of Science, Ceske Budejovice, Czech Republic.
| | - Apolline Maitre
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort F-94700, France; INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), 20250 Corte, France; EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Dasiel Obregón
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort F-94700, France
| | - Srinivas Thaduri
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden
| | - Barbara Locke
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden
| | - Lourdes Mateos-Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort F-94700, France
| | - Alena Bruce Krejčí
- University of South Bohemia, Faculty of Science, Ceske Budejovice, Czech Republic; Czech Academy of Sciences, Biology Centre, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort F-94700, France.
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3
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Heni AC, Fackelmann G, Eibner G, Kreinert S, Schmid J, Schwensow NI, Wiegand J, Wilhelm K, Sommer S. Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances. Anim Microbiome 2023; 5:22. [PMID: 37024947 PMCID: PMC10080760 DOI: 10.1186/s42523-023-00237-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Human encroachment into nature and the accompanying environmental changes are a big concern for wildlife biodiversity and health. While changes on the macroecological scale, i.e. species community and abundance pattern, are well documented, impacts on the microecological scale, such as the host's microbial community, remain understudied. Particularly, it is unclear if impacts of anthropogenic landscape modification on wildlife gut microbiomes are species-specific. Of special interest are sympatric, generalist species, assumed to be more resilient to environmental changes and which often are well-known pathogen reservoirs and drivers of spill-over events. Here, we analyzed the gut microbiome of three such sympatric, generalist species, one rodent (Proechimys semispinosus) and two marsupials (Didelphis marsupialis and Philander opossum), captured in 28 study sites in four different landscapes in Panama characterized by different degrees of anthropogenic disturbance. RESULTS Our results show species-specific gut microbial responses to the same landscape disturbances. The gut microbiome of P. semispinosus was less diverse and more heterogeneous in landscapes with close contact with humans, where it contained bacterial taxa associated with humans, their domesticated animals, and potential pathogens. The gut microbiome of D. marsupialis showed similar patterns, but only in the most disturbed landscape. P. opossum, in contrast, showed little gut microbial changes, however, this species' absence in the most fragmented landscapes indicates its sensitivity to long-term isolation. CONCLUSION These results demonstrate that wildlife gut microbiomes even in generalist species with a large ecological plasticity are impacted by human encroachment into nature, but differ in resilience which can have critical implications on conservation efforts and One Health strategies.
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Affiliation(s)
- Alexander Christoph Heni
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany.
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama.
| | - Gloria Fackelmann
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Georg Eibner
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Swetlana Kreinert
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Julian Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama
| | - Nina Isabell Schwensow
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Jonas Wiegand
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany.
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Veith T, Bleicker T, Eschbach-Bludau M, Brünink S, Mühlemann B, Schneider J, Beheim-Schwarzbach J, Rakotondranary SJ, Ratovonamana YR, Tsagnangara C, Ernest R, Randriantafika F, Sommer S, Stetter N, Jones TC, Drosten C, Ganzhorn JU, Corman VM. Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host. Virus Evol 2023; 9:vead024. [PMID: 37091898 PMCID: PMC10121206 DOI: 10.1093/ve/vead024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023] Open
Abstract
Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus-host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.
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Affiliation(s)
- Talitha Veith
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University Hospital, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Julia Schneider
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - S Jacques Rakotondranary
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Yedidya R Ratovonamana
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Cedric Tsagnangara
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | - Refaly Ernest
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | | | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, Ulm 89069, Germany
| | - Nadine Stetter
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, Hamburg 20359, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörg U Ganzhorn
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
- Labor Berlin, Charité—Vivantes GmbH, Sylter Straße 2, Berlin 13353, Germany
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5
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Neha SA, Salazar-Bravo J. Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus). BMC Microbiol 2023; 23:51. [PMID: 36858951 PMCID: PMC9979494 DOI: 10.1186/s12866-023-02778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing. RESULTS The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity. CONCLUSIONS Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.
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Affiliation(s)
- Sufia Akter Neha
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA.
- Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA.
| | - Jorge Salazar-Bravo
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA
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6
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Gavin PG, Kim KW, Craig ME, Hill MM, Hamilton-Williams EE. Multi-omic interactions in the gut of children at the onset of islet autoimmunity. MICROBIOME 2022; 10:230. [PMID: 36527134 PMCID: PMC9756488 DOI: 10.1186/s40168-022-01425-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome, has been associated with the development of multiple human conditions including type 1 diabetes (T1D). Viruses infecting the gastrointestinal tract, especially enteroviruses, are also thought to play an important role in T1D pathogenesis possibly via overlapping mechanisms. However, it is not known whether the microbiome and virome act together or which risk factor may be of greater importance at the time when islet autoimmunity is initiated. RESULTS Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D. We show strong age-related effects, with microbial and metaproteome diversity increasing with age while host antibody number and abundance declined with age. Mastadenovirus, which has been associated with a reduced risk of T1D, was associated with profound changes in the metaproteome indicating a functional shift in the microbiota. Multi-omic factor analysis modeling revealed a cluster of proteins associated with carbohydrate transport from the genus Faecalibacterium were associated with islet autoimmunity. CONCLUSIONS These findings demonstrate the interrelatedness of the gut microbiota, metaproteome and virome in young children. We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity. Video Abstract.
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Affiliation(s)
- Patrick G Gavin
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Present Address: Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Present Address: Harvard Medical School, Boston, MA, USA
| | - Ki Wook Kim
- Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Maria E Craig
- Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
- Institute of Endocrinology and Diabetes, Children's Hospital at Westmead, Sydney, Australia
- Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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The Kitty Microbiome Project: Defining the Healthy Fecal "Core Microbiome" in Pet Domestic Cats. Vet Sci 2022; 9:vetsci9110635. [PMID: 36423084 PMCID: PMC9698023 DOI: 10.3390/vetsci9110635] [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: 10/01/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Here, we present a taxonomically defined fecal microbiome dataset for healthy domestic cats (Felis catus) fed a range of commercial diets. We used this healthy reference dataset to explore how age, diet, and living environment correlate with fecal microbiome composition. Thirty core bacterial genera were identified. Prevotella, Bacteroides, Collinsella, Blautia, and Megasphaera were the most abundant, and Bacteroides, Blautia, Lachnoclostridium, Sutterella, and Ruminococcus gnavus were the most prevalent. While community composition remained relatively stable across different age classes, the number of core taxa present decreased significantly with age. Fecal microbiome composition varied with host diet type. Cats fed kibble had a slightly, but significantly greater number of core taxa compared to cats not fed any kibble. The core microbiomes of cats fed some raw food contained taxa not as highly prevalent or abundant as cats fed diets that included kibble. Living environment also had a large effect on fecal microbiome composition. Cats living in homes differed significantly from those in shelters and had a greater portion of their microbiomes represented by core taxa. Collectively our work reinforces the findings that age, diet, and living environment are important factors to consider when defining a core microbiome in a population.
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8
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Schmid DW, Fackelmann G, Wasimuddin, Rakotondranary J, Ratovonamana YR, Montero BK, Ganzhorn JU, Sommer S. A framework for testing the impact of co-infections on host gut microbiomes. Anim Microbiome 2022; 4:48. [PMID: 35945629 PMCID: PMC9361228 DOI: 10.1186/s42523-022-00198-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 02/07/2023] Open
Abstract
Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.
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Malik H, Ratovonamana YR, Rakotondranary SJ, Ganzhorn JU, Sommer S. Anthropogenic Disturbance Impacts Gut Microbiome Homeostasis in a Malagasy Primate. Front Microbiol 2022; 13:911275. [PMID: 35801106 PMCID: PMC9253676 DOI: 10.3389/fmicb.2022.911275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/19/2022] [Indexed: 12/05/2022] Open
Abstract
Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of gray-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species marked by a reduction in bacterial diversity and a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria (i.e., members of the Bacteroidaceae family) together with a slight increase in disease-associated bacteria (i.e., members of the Veillonellaceae family), and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to pathogen resistance and host health, such negative alterations in the gut microbiome of mouse lemurs inhabiting anthropogenically disturbed habitats might render them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.
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Affiliation(s)
- Hina Malik
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Yedidya R Ratovonamana
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
- Département Biologie Animale, Faculté des Sciences, Université d' Antananarivo, Antananarivo, Madagascar
| | - Solofomalala Jacques Rakotondranary
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
- Département Biologie Animale, Faculté des Sciences, Université d' Antananarivo, Antananarivo, Madagascar
| | - Jörg U Ganzhorn
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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10
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Mizutani T, Ishizaka A, Koga M, Tsutsumi T, Yotsuyanagi H. Role of Microbiota in Viral Infections and Pathological Progression. Viruses 2022; 14:950. [PMID: 35632692 PMCID: PMC9144409 DOI: 10.3390/v14050950] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.
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Affiliation(s)
- Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Evidence of MHC class I and II influencing viral and helminth infection via the microbiome in a non-human primate. PLoS Pathog 2021; 17:e1009675. [PMID: 34748618 PMCID: PMC8601626 DOI: 10.1371/journal.ppat.1009675] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/18/2021] [Accepted: 10/05/2021] [Indexed: 01/04/2023] Open
Abstract
Until recently, the study of major histocompability complex (MHC) mediated immunity has focused on the direct link between MHC diversity and susceptibility to parasite infection. However, MHC genes can also influence host health indirectly through the sculpting of the bacterial community that in turn shape immune responses. We investigated the links between MHC class I and II gene diversity gut microbiome diversity and micro- (adenovirus, AdV) and macro- (helminth) parasite infection probabilities in a wild population of non-human primates, mouse lemurs of Madagascar. This setup encompasses a plethora of underlying interactions between parasites, microbes and adaptive immunity in natural populations. Both MHC classes explained shifts in microbiome composition and the effect was driven by a few select microbial taxa. Among them were three taxa (Odoribacter, Campylobacter and Prevotellaceae-UCG-001) which were in turn linked to AdV and helminth infection status, correlative evidence of the indirect effect of the MHC via the microbiome. Our study provides support for the coupled role of MHC diversity and microbial flora as contributing factors of parasite infection. The selective pressure of the major histocompatibility complex (MHC) on microbial communities, and the potential role of this interaction in driving parasite resistance has been largely neglected. Using a natural population of the primate Microcebus griseorufus, we provide correlative evidence of two outstanding findings: that MHCI and MHCII diversity shapes the composition of the gut microbiota; and that select taxa associated with MHC diversity predicted adenovirus and helminth infection status. Our study highlights the importance of incorporating the microbiome when investigating parasite-mediated MHC selection.
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Abstract
In the Anthropocene, humans, domesticated animals, wildlife, and their environments are interconnected, especially as humans advance further into wildlife habitats. Wildlife gut microbiomes play a vital role in host health. Changes to wildlife gut microbiomes due to anthropogenic disturbances, such as habitat fragmentation, can disrupt natural gut microbiota homeostasis and make animals vulnerable to infections that may become zoonotic. However, it remains unclear whether the disruption to wildlife gut microbiomes is caused by habitat fragmentation per se or the combination of habitat fragmentation with additional anthropogenic disturbances, such as contact with humans, domesticated animals, invasive species, and their pathogens. Here, we show that habitat fragmentation per se does not impact the gut microbiome of a generalist rodent species native to Central America, Tome's spiny rat Proechimys semispinosus, but additional anthropogenic disturbances do. Indeed, compared to protected continuous and fragmented forest landscapes that are largely untouched by other human activities, the gut microbiomes of spiny rats inhabiting human-disturbed fragmented landscapes revealed a reduced alpha diversity and a shifted and more dispersed beta diversity. Their microbiomes contained more taxa associated with domesticated animals and their potential pathogens, suggesting a shift in potential metagenome functions. On the one hand, the compositional shift could indicate a degree of gut microbial adaption known as metagenomic plasticity. On the other hand, the greater variation in community structure and reduced alpha diversity may signal a decline in beneficial microbial functions and illustrate that gut adaption may not catch up with anthropogenic disturbances, even in a generalist species with large phenotypic plasticity, with potentially harmful consequences to both wildlife and human health.
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Yang M, Yang Y, He Q, Zhu P, Liu M, Xu J, Zhao M. Intestinal Microbiota-A Promising Target for Antiviral Therapy? Front Immunol 2021; 12:676232. [PMID: 34054866 PMCID: PMC8149780 DOI: 10.3389/fimmu.2021.676232] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiota is thought to be an important biological barrier against enteric pathogens. Its depletion, however, also has curative effects against some viral infections, suggesting that different components of the intestinal microbiota can play both promoting and inhibitory roles depending on the type of viral infection. The two primary mechanisms by which the microbiota facilitates or inhibits viral invasion involve participation in the innate and adaptive immune responses and direct or indirect interaction with the virus, during which the abundance and composition of the intestinal microbiota might be changed by the virus. Oral administration of probiotics, faecal microbiota transplantation (FMT), and antibiotics are major therapeutic strategies for regulating intestinal microbiota balance. However, these three methods have shown limited curative effects in clinical trials. Therefore, the intestinal microbiota might represent a new and promising supplementary antiviral therapeutic target, and more efficient and safer methods for regulating the microbiota require deeper investigation. This review summarizes the latest research on the relationship among the intestinal microbiota, anti-viral immunity and viruses and the most commonly used methods for regulating the intestinal microbiota with the goal of providing new insight into the antiviral effects of the gut microbiota.
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Affiliation(s)
- Mengling Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yang Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingnan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Mengqi Liu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jiahao Xu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mingyi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
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Risely A, Gillingham MAF, Béchet A, Brändel S, Heni AC, Heurich M, Menke S, Manser MB, Tschapka M, Wasimuddin, Sommer S. Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species. Front Microbiol 2021; 12:659918. [PMID: 34046023 PMCID: PMC8144293 DOI: 10.3389/fmicb.2021.659918] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
The filtering of gut microbial datasets to retain high prevalence taxa is often performed to identify a common core gut microbiome that may be important for host biological functions. However, prevalence thresholds used to identify a common core are highly variable, and it remains unclear how they affect diversity estimates and whether insights stemming from core microbiomes are comparable across studies. We hypothesized that if macroecological patterns in gut microbiome prevalence and abundance are similar across host species, then we would expect that increasing prevalence thresholds would yield similar changes to alpha diversity and beta dissimilarity scores across host species datasets. We analyzed eight gut microbiome datasets based on 16S rRNA gene amplicon sequencing and collected from different host species to (1) compare macroecological patterns across datasets, including amplicon sequence variant (ASV) detection rate with sequencing depth and sample size, occupancy-abundance curves, and rank-abundance curves; (2) test whether increasing prevalence thresholds generate universal or host-species specific effects on alpha and beta diversity scores; and (3) test whether diversity scores from prevalence-filtered core communities correlate with unfiltered data. We found that gut microbiomes collected from diverse hosts demonstrated similar ASV detection rates with sequencing depth, yet required different sample sizes to sufficiently capture rare ASVs across the host population. This suggests that sample size rather than sequencing depth tends to limit the ability of studies to detect rare ASVs across the host population. Despite differences in the distribution and detection of rare ASVs, microbiomes exhibited similar occupancy-abundance and rank-abundance curves. Consequently, increasing prevalence thresholds generated remarkably similar trends in standardized alpha diversity and beta dissimilarity across species datasets until high thresholds above 70%. At this point, diversity scores tended to become unpredictable for some diversity measures. Moreover, high prevalence thresholds tended to generate diversity scores that correlated poorly with the original unfiltered data. Overall, we recommend that high prevalence thresholds over 70% are avoided, and promote the use of diversity measures that account for phylogeny and abundance (Balance-weighted phylogenetic diversity and Weighted Unifrac for alpha and beta diversity, respectively), because we show that these measures are insensitive to prevalence filtering and therefore allow for the consistent comparison of core gut microbiomes across studies without the need for prevalence filtering.
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Affiliation(s)
- Alice Risely
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Mark A. F. Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Arnaud Béchet
- Institut de Recherche de la Tour du Valat, Le Sambuc, Arles, France
| | - Stefan Brändel
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Alexander C. Heni
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Marco Heurich
- Department of Visitor Management and National Park Monitoring, Bavarian Forest National Park, Grafenau, Germany
- Chair of Wildlife Ecology and Management, University of Freiburg, Freiburg, Germany
- Institute for Forest and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
| | - Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Marta B. Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Wasimuddin
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Porto BN, Moraes TJ. The triad: respiratory microbiome - virus - immune response in the pathophysiology of pulmonary viral infections. Expert Rev Respir Med 2021; 15:635-648. [PMID: 33605840 DOI: 10.1080/17476348.2021.1893168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The longstanding dogma that the healthy lung is sterile has been refuted by recent advances in culture-independent analyses of airway samples. The respiratory microbiome comprises all airway and lung tissue-associated microbes. These micro-organisms occur throughout the upper and lower respiratory tracts, with different populations and distinct burdens at specific sites and can be classified as pathogenic or commensal. AREAS COVERED The majority of studies investigating the respiratory microbiome have focused on bacteria; however, emerging evidence has revealed the composition of the lung virome, the global viral communities present in the lung tissue. In this review, we searched PubMed and used keywords such as airway microbiome. We restricted outputs to English language and did not limit by any dates. We summarize the up-to-date knowledge on how the microbiome interacts with the host immune system and influences the pathogenesis of pulmonary viral infections. EXPERT OPINION The relationship between colonizing microbes and the host is complex and various factors need to be considered in order to appreciate its pathophysiological consequences. Understanding these intricate mechanisms of interaction among the respiratory microbiome, viruses and the immune response may lead to the development of better therapies to treat or prevent respiratory viral infections.
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Affiliation(s)
- Bárbara N Porto
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Sadiq FA. Is it time for microbiome-based therapies in viral infections? Virus Res 2021; 291:198203. [PMID: 33132161 PMCID: PMC7580679 DOI: 10.1016/j.virusres.2020.198203] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 01/07/2023]
Abstract
Infectious diseases related to viruses, as well as bacterial pathogens, abound in all parts of the world, burdening health and economy. Thus, there is a dire need to find new prevention and treatment strategies to improve clinical practices related to viral infections. Human gut contains trillions of bacteria which have regulatory roles in immune development, homeostasis, and body metabolism. Today, it is difficult to find any prominent viral infection that hasn't had any link with the human gut microbiota. In this opinion-based review article, I argued the significance of manipulating human gut microbiota as novel therapeutics through probiotics or FMT in alleviating complexities related to viral infections, and pinpointed bottlenecks involved in this research.
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Affiliation(s)
- Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 1800 Lihu Avenue, 214122, China.
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The Effect of Transitioning between Feeding Methods on the Gut Microbiota Dynamics of Yaks on the Qinghai-Tibet Plateau. Animals (Basel) 2020; 10:ani10091641. [PMID: 32933061 PMCID: PMC7552143 DOI: 10.3390/ani10091641] [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: 08/06/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary This study explores the gut microbiota alterations that occur when transferring yaks from winter grassland to feedlot feeding, and to determine the adaptation period. Our results demonstrated that such transferring could influence the gut micro-ecology, and was stabilized within 16 days. This study will improve the understanding of the processes behind gut microbiota adaptation to an abrupt change in feeding methods, and will provide a reasonable adaptation period for yak management, which could be applied to nutritional research and minimize detrimental effects in the animals. Abstract Here we aimed to explore the change in yak gut microbiota after transferring yaks from grazing grassland to a feedlot, and determine their diet adaptation period. Five yaks were transferred from winter pasture to an indoor feedlot. Fecal samples were obtained from grazing (G) and feedlot feeding yaks at day 1 (D1), day 4 (D4), day 7 (D7), day 11 (D11), and day 16 (D16). The dynamic variation of the bacterial community was analyzed using 16S rRNA gene sequencing. The results showed that the yak gut microbial community structure underwent significant changes after diet transition. At the phylum and genus levels, most bacteria changed within D1–D11; however, no significant changes were observed from D11–D16. Furthermore, we used random forest to determine the key bacteria (at class level) disturbing gut micro-ecology. The relative abundance of the top four classes (Erysipelotrichia, Gammaproteobacteria, Saccharimonadia, and Coriobacteriia) was highest on D1–D4, and then decreased and plateaued over time. Our results demonstrated that an abrupt adjustment to a diet with high nutrition could influence the gut micro-ecology, which was stabilized within 16 days, thus providing insights into diet adaptation in the yak gut.
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Abstract
Due to its fundamental role in the induction, training, and function of the immune system, it is critical to include characterizations of the gut microbiome in clinical trials and studies that aim to broaden our understanding of coronavirus disease 2019 (COVID-19). Understanding the “gut-lung axes,” where gut microbiome composition influences the lung’s susceptibility to viral infections and viral infections of the lung alter gut microbiome composition toward proinflammatory functional dysbiosis, will be critical in addressing COVID-19, including disease progression, the importance of preexisting conditions, and the risk for developing complications. Due to its fundamental role in the induction, training, and function of the immune system, it is critical to include characterizations of the gut microbiome in clinical trials and studies that aim to broaden our understanding of coronavirus disease 2019 (COVID-19). Understanding the “gut-lung axes,” where gut microbiome composition influences the lung’s susceptibility to viral infections and viral infections of the lung alter gut microbiome composition toward proinflammatory functional dysbiosis, will be critical in addressing COVID-19, including disease progression, the importance of preexisting conditions, and the risk for developing complications. These insights may further help to develop better intervention strategies for COVID-19 and other diseases caused by respiratory viruses.
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Bots ST, Hoeben RC. Non-Human Primate-Derived Adenoviruses for Future Use as Oncolytic Agents? Int J Mol Sci 2020; 21:ijms21144821. [PMID: 32650405 PMCID: PMC7404033 DOI: 10.3390/ijms21144821] [Citation(s) in RCA: 16] [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: 06/15/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
Non-human primate (NHP)-derived adenoviruses have formed a valuable alternative for the use of human adenoviruses in vaccine development and gene therapy strategies by virtue of the low seroprevalence of neutralizing immunity in the human population. The more recent use of several human adenoviruses as oncolytic agents has exhibited excellent safety profiles and firm evidence of clinical efficacy. This proffers the question whether NHP-derived adenoviruses could also be employed for viral oncolysis in human patients. While vaccine vectors are conventionally made as replication-defective vectors, in oncolytic applications replication-competent viruses are used. The data on NHP-derived adenoviral vectors obtained from vaccination studies can only partially support the suitability of NHP-derived adenoviruses for use in oncolytic virus therapy. In addition, the use of NHP-derived adenoviruses in humans might be received warily given the recent zoonotic infections with influenza viruses and coronaviruses. In this review, we discuss the similarities and differences between human- and NHP-derived adenoviruses in view of their use as oncolytic agents. These include their genome organization, receptor use, replication and cell lysis, modulation of the host’s immune responses, as well as their pathogenicity in humans. Together, the data should facilitate a rational and data-supported decision on the suitability of NHP-derived adenoviruses for prospective use in oncolytic virus therapy.
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