You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches

Melissa R Ingala; Nancy B Simmons; Miranda Dunbar; Claudia Wultsch; Konstantinos Krampis; Susan L Perkins

doi:10.1186/s42523-021-00139-8

You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches

Anim Microbiome. 2021 Dec 14;3(1):82. doi: 10.1186/s42523-021-00139-8.

Authors

Melissa R Ingala^{1

2

3}, Nancy B Simmons⁴, Miranda Dunbar⁵, Claudia Wultsch^{6

7}, Konstantinos Krampis^{7

8

9}, Susan L Perkins^{10

6}

Affiliations

¹ Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, USA. ingala.melissar@gmail.com.
² Department of Mammalogy, The American Museum of Natural History, New York, NY, USA. ingala.melissar@gmail.com.
³ Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY, USA. ingala.melissar@gmail.com.
⁴ Department of Mammalogy, The American Museum of Natural History, New York, NY, USA.
⁵ Department of Biological Sciences, Southern Connecticut State University, New Haven, CT, USA.
⁶ Sackler Institute for Comparative Genomics, The American Museum of Natural History, New York, NY, USA.
⁷ Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY, USA.
⁸ Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA.
⁹ Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA.
¹⁰ Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY, USA.

Abstract

Background: Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts and their gut bacteria, fewer studies examine the potentially adaptive functional contributions of these microbes to the dietary habits of their hosts. In this study, we examined predicted metabolic pathways in the gut bacteria of more than 500 individual bats belonging to 60 species and compare the enrichment of these functions across hosts with distinct dietary ecologies.

Results: We found that predicted microbiome functions were differentially enriched across hosts with different diets. Using a machine-learning approach, we also found that inferred microbiome functions could be used to predict specialized host diets with reasonable accuracy. We detected a relationship between both host phylogeny and diet with respect to microbiome functional repertoires. Because many predicted functions could potentially fill nutritional gaps for bats with specialized diets, we considered pathways discriminating dietary niches as traits of the host and fit them to comparative phylogenetic models of evolution. Our results suggest that some, but not all, predicted microbiome functions may evolve toward adaptive optima and thus be visible to the forces of natural selection operating on hosts over evolutionary time.

Conclusions: Our results suggest that bats with specialized diets may partially rely on their gut microbes to fulfill or augment critical nutritional pathways, including essential amino acid synthesis, fatty acid biosynthesis, and the generation of cofactors and vitamins essential for proper nutrition. Our work adds to a growing body of literature suggesting that animal microbiomes are structured by a combination of ecological and evolutionary processes and sets the stage for future metagenomic and metabolic characterization of the bat microbiome to explore links between bacterial metabolism and host nutrition.

Keywords: 16S rRNA gene; Bats; Dietary ecology; Evolution; Functional prediction; Microbiome.

Abstract

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