Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores
Authors: Meili Casey H. , TagElDein Moustafa A. , Jones Adrienne L. , Moon Christina D. , Andrews Catherine , Kirk Michelle R. , Janssen Peter H. , J. Yeoman Carl , Grace Savannah , Borgogna Joanna-Lynn C. , Foote Andrew P. , Nagy Yosra I. , Kashef Mona T. , Yassin Aymen S. , Elshahed Mostafa S. , Youssef Noha H. 
Published: February 2024

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (
Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces,
NY9, and
Piromyces
) were present at >4% relative abundance. AGF diversity was higher in members of the families
Antilocapridae
and
Cervidae
compared to
Bovidae
. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%–19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (
n
= 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera
Neocallimastix
and
Orpinomyces
were present in higher abundance in rumen samples, while
Cyllamyces
and
Caecomyces
were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.

IMPORTANCE

Ruminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum
Neocallimastigomycota
. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (
n
= 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (
Neocallimastix
and
Orpinomyces
) present in higher abundance in rumen samples, and two others (
Cyllamyces
and
Caecomyces
) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.