A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework

Paul, Souvik; Bu, Dengpan; Xu, Jianchu; Hyde, Kevin D.; Yu, Zhongtang

doi:10.1007/s13225-018-0396-6

Cited by 47 publications

(70 citation statements)

References 62 publications

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“…Collectively, the steady identification of novel taxa in culture-based and culture-independent surveys, as well as the sparse overlap between these studies strongly suggests that the scope of AGF diversity in nature is much broader than currently estimated (Kittelmann and others 2012; Paul and others 2018). Compared to the prokaryotic component of the rumen and herbivorous gut, the diversity of the rumen mycobiome remains woefully understudied.…”

Section: Discussionmentioning

confidence: 99%

“…We queried GenBank and ITS-1 datasets (Kittelmann and others 2012; Liggenstoffer and others 2010; Paul and others 2018) using reference ITS-1 sequences from strains recovered in this study. The phylogenetic position of all closely related sequences (> 87% sequence similarity) was evaluated by insertion into maximum likelihood trees.…”

Section: Methodsmentioning

confidence: 99%

“…The phylogenetic position of all closely related sequences (> 87% sequence similarity) was evaluated by insertion into maximum likelihood trees. Taxonomy of uncultured taxa followed the schemes outlined in prior publications (Kittelmann and others 2012; Liggenstoffer and others 2010; Paul and others 2018).…”

Section: Methodsmentioning

confidence: 99%

“…Further, it is entirely plausible that multiple AGF taxa are extremely fastidious, with complex nutritional requirements that are not satisfied in current isolation protocols. Indeed, culture-independent diversity surveys utilizing the internal transcribed spacer 1 (ITS-1) as a phylogenetic marker demonstrated that multiple novel AGF lineages remain to be isolated and characterized (Kittelmann and others 2012; Liggenstoffer and others 2010; Paul and others 2018; Mura and others 2019).…”

Section: Introductionmentioning

confidence: 99%

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Seven new Neocallimastigomycota genera from fecal samples of wild, zoo-housed, and domesticated herbivores: Description ofGhazallomyces constrictusgen. nov., sp. nov.,Aklioshbomyces papillarumgen. nov., sp. nov.,Agriosomyces longusgen. nov., sp. nov.,Capellomyces foraminisgen. nov., sp. nov. andCapellomyces elongatussp. nov.,Joblinomyces apicalisgen. nov., sp. nov.,Khoyollomyces ramosusgen. nov., sp. nov., andTahromyces munnarensisgen. nov., sp. nov

Hanafy

Lanjekar

Dhakephalkar

et al. 2019

Preprint

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We isolated and characterized sixty-five anaerobic gut fungi (AGF, Neocallimastigomycota) strains from fecal samples of five wild (W), one zoo-housed (Z), and three domesticated (D) herbivores in the US states of Texas (TX) and Oklahoma (OK), Wales (WA), and the Indian states of Kerala (KE) and Haryana (HA). Phylogenetic assessment based on D1-D2 region of the large rRNA subunit (LSU) identified seven distinct lineages, with strains recovered from Axis Deer (W-TX) clustering within the Orpinomyces-Neocallimastix-Pecoramyces-Feramyces clade; Boer Goat-domesticated Goat strains (W-TX, D-KE) clustering within the Oontomyces-Anaeromyces-Liebetanzomyces clade; and domesticated Goat and Sheep strains (D-HA) as well as Nilgiri Tahr strains (W-KE) forming two distinct clades associated with genus Buwchfawromyces. The remaining three lineages, represented by strains recovered from Mouflon-Boer Goat (W-TX), White Tailed Deer (W-OK), and Zebra-Horse (Z-OK, and D-WA), displayed no specific suprageneric affiliation. All strains displayed monocentric thalli and produced mono/uniflagellate zoospores with the exception of Axis Deer strains, which produced polyflagellate zoospores. Isolates displayed multiple interesting microscopic features including sporangia with tightly constricted necks and fine septa at the base (Axis Deer), papillated and pseudo-intercalary sporangia (White-Tailed Deer), swollen sporangiophores and zoospores with long flagella (Mouflon-Boer Goat), zoospore release through an apical pore followed by either sporangial wall collapse (Axis Deer and Boer Goat-domesticated Goat) or sporangial wall remaining intact after discharge (Zebra-Horse), multi-sporangiated thalli with branched sporangiophores (Zebra-Horse), and short sporangiophores with subsporangial swellings (Nilgiri Tahr). Internal transcribed spacer-1 region (ITS-1) sequence analysis indicated that Zebra-Horse strains are representatives of the AL1 lineage, frequently encountered in culture-independent surveys of the alimentary tract and fecal samples from hindgut fermenters. The other six lineages, five of which were isolated from wild herbivores, have not been previously encountered in such surveys. Our results significantly expand the genus level diversity within the Neocallimastigomycota, and strongly suggest that wild herbivores represent a yet-untapped reservoir of AGF diversity. We propose the creation of seven novel genera and eight novel Neocallimastigomycota species to accommodate these strains, for which we propose the names Agriosomyces longus (Mouflon and wild Boer Goat), Aklioshbomyces papillarum (White tailed Deer), Capellomyces foraminis (wild Boar Goat) and C. elongatus (domesticated Goat), Ghazallomyces constrictus (Axis Deer), Joblinomyces apicalis (domesticated Goat and Sheep), Khoyollomyces ramosus (Zebra-Horse), and Tahromyces munnarensis (Nilgiri Tahr). The type species are strains Axs-31, WT-2, MS-4, BGB-11, GFKJa1916, GFH683, ZS-33, and TDFKJa193, respectively.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Seven new Neocallimastigomycota genera from fecal samples of wild, zoo-housed, and domesticated herbivores: Description ofGhazallomyces constrictusgen. nov., sp. nov.,Aklioshbomyces papillarumgen. nov., sp. nov.,Agriosomyces longusgen. nov., sp. nov.,Capellomyces foraminisgen. nov., sp. nov. andCapellomyces elongatussp. nov.,Joblinomyces apicalisgen. nov., sp. nov.,Khoyollomyces ramosusgen. nov., sp. nov., andTahromyces munnarensisgen. nov., sp. nov

Hanafy

Lanjekar

Dhakephalkar

et al. 2019

Preprint

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“…Reported counts of fungal cells vary greatly between studies, with numbers ranging between 10 3 and 10 6 cells/ml of rumen fluid [14][15][16] . To date, only a total of eighteen genera (Agriosomyces, Aklioshbomyces, Anaeromyces, Buwchfawromyces, Caecomyces, Capellomyces, Ghazallomyces, Cyllamyces, Feramyces, Joblinomyces, Khoyollomyces, Neocallimastix, Liebetanzomyces, Oontomyces, Orpinomyces, Pecoramyces, Piromyces, and Tahromyces), all belonging to the early-branching phylum Neocallimastigomycota, have been described 4,[17][18][19] , although culture independent studies have suggested that this only represents half of the anaerobic fungal population that exist in the rumen ecosystem 17,20 . Genomes obtained from representatives of this phylum have been recognized to encode a large number of biomass-degrading enzymes and it is becoming increasingly clear that these currently still understudied organisms play a key role in the anaerobic digestion of complex plant carbohydrates 4,10,21 .…”

Section: Introductionmentioning

confidence: 99%

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Hagen

Brooke

Shaw

et al. 2020

Preprint

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The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo-and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryoteselected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

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Comparative Assessment of Rumen Microbial Diversity in Cattle and Buffaloes

Malik

Trivedi

Kolte

et al. 2021

Climate Change and Livestock Production: Recent Advances and Future Perspectives

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A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework

Cited by 47 publications

References 62 publications

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Comparative Assessment of Rumen Microbial Diversity in Cattle and Buffaloes

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