Variability of treponemes in the rumen of ruminants

Abstract

Complete 16S rRNA sequences were determined of recently proposed new species of treponemes designated strain S and T. Sequence comparison indicated that both species belong to the Treponema saccharophilum cluster, having thus at least 5 cultivable representatives. Phylogenetic analysis of available GenBank 16S rRNA sequences revealed two phylogenetically distant treponema clusters (T. saccharophilum cluster and T. bryantii cluster). Surprisingly, while among cultivated treponemes dominate T. saccharophilum cluster members, detailed analysis showed that all treponema-like sequences obtained by culture independent 16S rRNA methods belong to the T. bryantii cluster, from which only two cultivable representatives have so far been known. Meta-analysis of available data revealed that treponemes are an infrequent and minor group of bacteria, representing less than 2.4% of total rumen bacteria.

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

“…Treponema has been estimated to account for less than 2.4% of the bovine rumen bacterial community (Sikorová et al , 2010), but as described above, our results suggest that species of this genus are more abundant in the moose rumen. All MAGs of phylum Spirochaetes were of genus Treponema and resembled closely with Treponema saccharophilum, a pectinolytic bacterium isolated from bovine rumen (Paster and Canale-Parola, 1985).…”

Monitoring the rumen pectinolytic bacteriaTreponema saccharophilumusing real-time PCR

“…A meta‐analysis of available data conducted by Sikorova et al . () revealed that the Treponem a genus represented < 2.4% of total rumen bacteria.…”

“…Prior to this study, only one 16S rRNA gene sequence (accession number ), with 98% similarity to T. saccharophilum , had been deposited in the GenBank database. The lack of T. saccharophilum‐ like 16S rRNA gene sequences in the available databases or published studies has been recognized in recent papers (Sikorova et al ., ; Bekele et al ., ). One possible explanation is that the Treponema genus was not well discussed due to its relative low abundance.…”

“…Prior to this study, only one 16S rRNA gene sequence (accession number HM049827), with 98% similarity to T. saccharophilum, had been deposited in the GenBank database. The lack of T. saccharophilum-like 16S rRNA gene sequences in the available databases or published studies has been recognized in recent papers (Sikorova et al, 2010;Bekele et al, 2011). One possible explanation is that the Treponema genus was not well discussed due to its relative low Next-generation sequencing platforms, such as 454 pyrosequencing, have been recognized as a more reliable quantitative analysis method than the reproducibilitydubious clone libraries (Acinas et al, 2005).…”

“…S , Treponema sp. CA, Treponema zioleckii KT, and Treponema succinifaciens DSM 2489) previously reported (Sikorova et al ., ) to be closely related to T. saccharophilum were considered nontarget species. Specific primer pairs were manually designed and analyzed using oligo Primer Analysis Software, version 6.0 (Rychlik & Rhoads, ) based on the alignment of target and nontarget species sequences using clustalw (Thompson et al ., ) with forward and reverse primers targeting positions 482–501 and 925–947 in the T. saccharophilum 16S rRNA gene sequence, respectively.…”