Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses

Ganz, Holly H.; Doroud, Ladan; Firl, Alana; Hird, Sarah M.; Eisen, Jonathan A.; Boyce, Walter M.

doi:10.1128/msystems.00188-16

Cited by 47 publications

(60 citation statements)

References 58 publications

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“…Haemophilus is a well-known bacterial genus that harbours many pathogenic species such as H. influenzae, which shows an increased presence in gut diseases (e.g. Crohn's disease; [46]) or after influenza virus infection [47]. The family of Enterobacteriaceae harbour many pathogenic and commensal species (e.g.…”

Section: Discussionmentioning

confidence: 99%

Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats

Wasimuddin

Brändel

Tschapka

et al. 2018

ISME J

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Astroviruses (AstV) are a major cause of diarrhoea in children. Interestingly, some wildlife species, including bats, remain phenotypically asymptomatic after infection. Disease symptoms, however, may only be less visible in bats and enteric viruses may indeed perturb their gut microbial communities. Gut microbiomes represent an important driver of immune defence mechanisms but potential effects of enteric virus-host microbiome interactions are largely unexplored. Using bats as a natural model system, we show that AstV-infections affect the gut microbiome, with the strength of the effect depending on host age. The gut microbial α- and β-diversity and the predicted microbial functional orthologs decreased in young bats but surprisingly increased in adult AstV + bats. The abundance of bacterial taxa characteristic for healthy microbiomes was strongly reduced in young AstV+ bats, possibly attributable to their immature immune system. Regardless of age, pathogen-containing genera exhibited negative interactions with several commensal taxa and increased after AstV-infection, leading to pathobiont-like shifts in the gut microbiome of all infected bats. Thus, in apparently healthy bats, AstV-infections disturb gut bacterial homeostasis, possibly increasing previously suppressed health risks by promoting co-infections. If similar processes are present in humans, the effects of enteric virus infections might have longer-term impacts extending beyond the directly observed symptoms.

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Section: Discussionmentioning

confidence: 99%

Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats

Wasimuddin

Brändel

Tschapka

et al. 2018

ISME J

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“…A large number of studies investigating the gut microbiome of birds and reptiles have sampled bacteria from the cloaca (Allegretti et al., ; Barbosa et al., ; Bowman & Jacobson, ; Charruau, Pérez‐Flores, Pérez‐Juárez, Cedeño‐Vázquez, & Rosas‐Carmona, ; Cooper, Needham, & Lawrence, ; D'Aloia, Bailey, Samour, Naldo, & Howlett, ; Dewar, Arnould, Krause, Dann, & Smith, ; Dewar et al., ; Dickinson, Duck, Schwalbe, Jarchow, & Trueblood, ; van Dongen et al., ; Ganz et al., ; Hoar, Whiteside, Ward, Inglis, & Morck, ; Klomp et al., ; Kreisinger, Čížková, Kropáčková, & Albrecht, ; Lamberski, Hull, Fish, Beckmen, & Morishita, ; Lobato, Geraldes, Melo, Doutrelant, & Covas, ; Lombardo et al., ; Lucas & Heeb, ; Martin, Gilman, & Weiss, ; Matson, Versteegh, van der Velde, & Tieleman, ; Maul, Gandhi, & Farris, ; Merkeviciene et al., ; Mills, Lombardo, & Thorpe, ; Moreno et al., ; Ruiz‐Rodríguez, Lucas, Heeb, & Soler, ; Ruiz‐Rodríguez, Soler, et al., ; Santoro, Hernández, & Caballero, ; Santos et al., ; Stanley, Geier, Chen, Hughes, & Moore, ; Stenkat, Krautwald‐Junghanns, Schmitz Ornés, Eilers, & Schmidt, ; Xenoulis et al., ). Cloacal sampling is widely used because it is straightforward to perform, allows repeated sampling of individuals and affords the possibility of reliably obtaining samples from all individuals at the same time.…”

Section: Introductionmentioning

confidence: 99%

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

Videvall

Strandh

Engelbrecht³

et al. 2017

Molecular Ecology Resources

126

162

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The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

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“…Jani & Briggs, ; Mshelia et al, ). Host characteristics such as sex, body condition and the presence or absence of pathogens are recognized as important for shaping microbial communities (Britton & Young, ; Cheng et al, ; Ganz et al, ; Hooper, Littman, & Macpherson, ; Jani & Briggs, , ; McKenney et al, ; Mshelia et al, ; Näpflin & Schmid‐Hempel, ). For example, horses in poor body condition have greater microbial diversity and a different suite of microbial species present compared to horses in good body condition (Mshelia et al, ).…”

Section: Introductionmentioning

confidence: 99%

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Fountain-Jones

Clark

Kinsley

et al. 2020

Journal of Animal Ecology

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Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free‐living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non‐model hosts.

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Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses

Cited by 47 publications

References 58 publications

Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats

Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

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