Species identity dominates over environment in shaping the microbiota of small mammals

Knowles, Sarah C. L.; Eccles, Richard; Baltrūnaitė, Laima

doi:10.1111/ele.13240

Cited by 104 publications

(114 citation statements)

References 80 publications

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“…Host genetics, rather than environmental factors, can explain differences in gut microbiota (Knowles, Eccles, & Baltrunaite, ). However, Darwin's finches, especially ground finches, are quite closely related (Chaves et al., ; Lamichhaney et al., ; Mckay & Zink, ), suggesting that the genomic underpinnings of the observed differences in the microbiota are unlikely.…”

Section: Discussionmentioning

confidence: 99%

Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands

2019

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The gut microbiota of animal hosts can be influenced by environmental factors, such as unnatural food items that are introduced by humans. Over the past 30 years, human presence has grown exponentially in the Galapagos Islands, which are home to endemic Darwin's finches. Consequently, humans have changed the environment and diet of Darwin's finches, which in turn, could affect their gut microbiota. In this study, we compared the gut microbiota of two species of Darwin's finches, small ground finches (Geospiza fuliginosa) and medium ground finches (Geospiza fortis), across sites with and without human presence, where finches prefer human‐processed and natural food, respectively. We predicted that: (a) finch microbiota would differ between sites with and without humans due to differences in diet, and (b) gut microbiota of each finch species would be most similar where finches have the highest niche overlap (areas with humans) compared to the lowest niche overlap (areas without humans). We found that gut bacterial community structure differed across sites and host species. Gut bacterial diversity was most distinct between the two species at the site with human presence compared to the site without human presence, which contradicted our predictions. Within host species, medium ground finches had lower bacterial diversity at the site with human presence compared to the site without human presence and bacterial diversity of small ground finches did not differ between sites. Our results show that the gut microbiota of Darwin's finches is affected differently across sites with varying human presence.

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Section: Discussionmentioning

confidence: 99%

Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands

2019

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“…Nevertheless, genetics and the resulting physiological differences may still have a role in shaping the microbiome. When the microbiomes of different species of non-human primates or small mammals are analysed, the strongest determinant of differences in the microbiome was evolutionary distance rather than diet, indicating that major differences in gut niches exist, due to genetic factors between these organisms 160,161 . This suggests that genetics has a potentially interesting and important role in shaping the microbiome, and genome-wide association studies (GWAS) could provide evidence for this role.…”

Section: Box 1 | Forces Shaping the Gut Microbiomementioning

confidence: 99%

Diet–microbiota interactions and personalized nutrition

2019

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Conceptual scientific and medical advances have led to a recent realization that there may be no single, one-size-fits-all diet and that differential human responses to dietary inputs may rather be driven by unique and quantifiable host and microbiome features. Integration of these person-specific host and microbiome readouts into actionable modules may complement traditional food measurement approaches in devising diets that are of benefit to the individual. Although many host-derived factors are hardwired and difficult to modulate, the microbiome may be more readily reshaped by environmental factors such as dietary exposures and is increasingly recognized to potentially impact human physiology by participating in digestion, the absorption of nutrients, shaping of the mucosal immune response and the synthesis or modulation of a plethora of potentially bioactive compounds. Thus, diet-induced microbiota alterations may be harnessed in order to induce changes in host physiology , including disease development and progression. However, major limitations in 'big-data' processing and analysis still limit our interpretive and translational capabilities concerning these person-specific host, microbiome and diet interactions. In this Review , we describe the latest advances in understanding dietmicrobiota interactions, the individuality of gut microbiota composition and how this knowledge could be harnessed for personalized nutrition strategies to improve human health.

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“…We then processed pair-end reads in Mothur using a standardized amplicon processing pipeline [38], aligned sequences to the silva v132 reference database [39] and assigned taxonomy to operational taxonomic units (OTUs) clustered using OptiClust [40] based on a 97% cut-off. To remove potential contaminants or sequencing errors, all nonbacterial OTUs and OTUs which were not represented by at least 1 read in 10% of the samples were removed prior to analysis, similar to Knowles et al [41]. OTUs were selected rather than exact sequence variants (ESVs) as we were interested primarily in identifying putative functional mechanisms underlying microbiome variation.…”

Section: (D) Sequencing and Bioinformaticsmentioning

confidence: 99%

It's what's on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal

2019

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The microbiome's capacity to shape the host phenotype and its mutability underlie theorization that the microbiome might facilitate host acclimation to rapid environmental change. However, when environmental change occurs, it is unclear whether resultant microbiome restructuring is proximately driven by this changing external environment or by the host's physiological response to this change. We leveraged urbanization to compare the ability of host environment (urban or forest) versus multi-scale biological measures of host hypothalamic–pituitary–adrenal (HPA) axis physiology (neutrophil : lymphocyte ratio, faecal glucocorticoid metabolites, hair cortisol) to explain variation in the eastern grey squirrel ( Sciurus carolinensis ) faecal microbiome. Urban and forest squirrels differed across all three of the interpretations of HPA axis activity we measured. Direct consideration of these physiological measures better explained greater phylogenetic turnover between squirrels than environment. This pattern was strongly driven by trade-offs between bacteria which specialize on metabolizing digesta versus host-derived nutrient sources. Drawing on ecological theory to explain patterns in intestinal bacterial communities, we conclude that although environmental change can affect the microbiome, it might primarily do so indirectly by altering host physiology. We demonstrate that the inclusion and careful consideration of dynamic, rather than fixed (e.g. sex), dimensions of host physiology are essential for the study of host–microbe symbioses at the micro-evolutionary scale.

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Species identity dominates over environment in shaping the microbiota of small mammals

Cited by 104 publications

References 80 publications

Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands

Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands

Diet–microbiota interactions and personalized nutrition

It's what's on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal

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