The Composition of Fungal Communities in the Rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow Cattle (Bos taurs)

Abstract

The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.

Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?

“…More than 90% of fungi sequences isolated in the rumen remain unclassified [54], however, the presence of anaerobic fungi belonging to phylum Neocallimastigomycetes (genera Neocallimastix, Caecomyces, Piromyces, Anaeromyces, Orpinomyces, and Cyllamyces) is acknowledged [55]. Fungi are infrequently found in strained rumen fluid because zoospores attach and colonize (encyst and germinate to produce the fungal thallus) the plant fragments suspended in the rumen natural digesta, being only then released by the sporangia [56].…”

Interrelationships of Fiber-Associated Anaerobic Fungi and Bacterial Communities in the Rumen of Bloated Cattle Grazing Alfalfa

“…We identified eight distinct genera of the phylum Neocallimastigomycetes, including Neocallimastix, Caecomyces, Piromyces, Anaeromyces, Orpinomyces, Cyllamyces , and Buwchfawromyces in over 80% of the ruminal samples collected from steers on both baseline and alfalfa pasture. Studies using ITS1 primer sets different than the one used in the present study have reported recovery of less than 23% of the sequencing reads assigned to ARF [ 19 ] and identified fewer ARF genera, including Piromyces, Anaeromyces, Cyllamyces, Neocallimastix , Caecomyces, and Orpionmyces [ 19 , 42 ]. By using a similar primer set to our study, Kumar et al [ 22 ] reported recovery of around 1% of the sequencing reads belonging to ARF and identified three genera within this phylum, including Cyllamyces, Caecomyces, and Orpinomyces .…”

“…Currently, ARF are classified into 18 distinct genera belonging to the phylum Neocallimastigomycota [18]. Among these, Neocallimastix, Piromyces, Caecomyces, Cyllamyces, Orpinomyces, Anaeromyces, Pecoramyces, and Buwchfawromyces have been previously identified in the rumen and fecal contents of cattle using a combination of culture-dependent and marker-gene sequencing methodologies [19][20][21][22][23]. These genera can be distinguished by morphological features, or through genetic variations in the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) locus [24,25].…”

Effect of the ratio of dietary metabolizable energy to nitrogen content on production performance, serum metabolites, rumen fermentation parameters, and bacterial diversity in yaks

“…The reason for this inconsistent pattern in the relative abundance of Acetitomaculum is uncertain and requires further research. Studies have demonstrated that there are substantial differences in rumen microbial structure and diversity between yaks and cattle ( An et al, 2005 ; Huang et al, 2012 ; Wang et al, 2019b ). Therefore, there are differences in the utilization of nutrient substrates between bovine species and different relationships may be formed between the host and microorganisms.…”