Editorial: Advances in the Understanding of the Commensal Eukaryota and Viruses of the Herbivore Gut

Gilbert, Rosalind A.; Dagar, Sumit Singh; Kittelmann, Sandra; Edwards, Joan E.

doi:10.3389/fmicb.2021.619287

Cited by 6 publications

(2 citation statements)

References 6 publications

(6 reference statements)

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“…The limited fungal communities were dominated by Ascomycota, followed by Basidiomycota, and Mucoromycota, similar to those reported in other herbivore guts except ruminants or ruminant-like mammals . However, the most noteworthy result, which supports the original hypothesis of this study, is that the AF group Neocallimastigomycota, abundant in herbivore, ruminant, and ruminant-like guts (8-20% of the total microbial biomass) 20,21,26,32,[42][43][44] , was insignificant or absent in metagenomic, metatranscriptomic, and metabarcoding data. In addition, shotgun metagenomic results showed that microbial (prokaryotes and eukaryotes) CAZy COGs, including glycoside hydrolases (GHs), were in very low abundance, 5-15´ less than reported for other ruminant or ruminant-like gut microbiomes 39,[45][46][47][48] .…”

Section: Discussionsupporting

confidence: 86%

Reduced functional fungal communities in two species of sloths (Bradypus variegatusandCholoepus hoffmanni) suggest a link to slow digestion

Chaverri,

Escudero-Leyva,

Mora-Rojas

et al. 2024

Preprint

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Sloths, with their ruminant-like digestive systems, possess the slowest digestion among mammals due to their low metabolic rate, minimal food intake, and extremely low-energy diet. However, no comprehensive studies have characterized the sloth’s gut microbiota, including fungi, and their role in digestion. This study hypothesized that effective plant fiber-degrading fungi (e.g., Neocallimastigomycota) would be scarce in the sloth’s gut. The aim was to describe the gut microbiota of three-toed (Bradypus variegatus) and two-toed (Choloepus hoffmanni) sloths to understand their link to slow digestion. Microbial composition and functionality were analyzed using shotgun metagenomics, metatranscriptomics, fungal metabarcoding (ITS 1 and 2 nrDNA), and cellulose degradation analysis. Microbial communities were dominated by bacteria (92–97%), followed by viruses (1–7%). Fungi accounted for only 0.06–0.5% of metagenomic reads and 0.1% of transcripts. Functional analysis revealed minimal CAZy abundance (1.7–1.9% in metagenomes, 0.2% in metatranscriptomes), with no fungal CAZys or glycoside hydrolases detected. Neocallimastigomycota had negligible abundance in metagenomic data and was absent in metatranscriptomic or ITS metabarcoding data.Bradypus variegatusshowed overall lower CAZy abundance and fungal presence compared toCholoepus hoffmanni. Lastly, cellulose degradation analyses revealed that only ∼5–35% of the intake was digested. This study highlights the unique microbial ecosystem in sloths’ guts, showing minimal presence of plant fiber-degrading anaerobic fungi and limited microbial CAZys, aligning with their slow digestion and low metabolic rate, thus enhancing our understanding of their digestive efficiency and metabolic adaptations.

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Section: Discussionsupporting

confidence: 86%

Reduced functional fungal communities in two species of sloths (Bradypus variegatusandCholoepus hoffmanni) suggest a link to slow digestion

Chaverri,

Escudero-Leyva,

Mora-Rojas

et al. 2024

Preprint

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“…However there is likely limited data on this phylum because Archaea are hard to culture and identify [32]. The remaining phyla are comprised of fungi, protozoa, viruses, and invertebrates, of which fungi and protozoa have been linked to digestive functions while viruses and invertebrates impact microbial diversity [35][36][37][38][39][40].…”

Section: Discussionmentioning

confidence: 99%

Diet and Domestication Drive Evolution of the Gut Holobiome

Ramanan

Mechery

Sarkar

2021

Preprint

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The host microbiome encompasses all microorganisms of a host. Host and microbiome coevolution in the gut result in differing microbial compositions, functionality, and host diet [1]. Host diet modulates what macromolecules are used for gut microbial metabolism, which can determine digestion, health, and behavior [2, 3]. Microbial composition across animals provides data on how microbiomes segregate between species and diets [4]. Here we show that microbiome data from GenBank can model host evolution, providing a holobiome insight to the important roles of diet and domestication. The main findings of this study in respect to microbial composition among species were: (1) herbivores are more similar than hosts with other diets; (2) domesticated species are more similar than wild relatives; and (3) humans are distinct from primates. Microbial composition between diets indicates a difference in functionality, where protein and fiber degradation are seen more in carnivores and herbivores respectively. Additionally, herbivores show the most microbial diversity among the diets. Finally, this analysis informs us of gaps in current microbiome data collection, which is biased toward pathogens. Thus, the host-microbiome relationship depicts a complex web of microbial functionality, composition, and diet that impact coevolution.

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