Genetic Diversity and Phylogenetic Relationships among Strains of Prevotella (Bacteroides) ruminicola from the Rumen

Abstract

A high degree of genetic diversity among 29 strains of Prevotella (Bacteroides) ruminicola from the rumen was revealed by comparing restriction fragment length polymorphisms in 16s rRNA genes, sodium dodecyl sulfate-polyacrylamide gel profiles of total-cell proteins, and G+ C contents of chromosomal DNAs. In order to obtain information on phylogenetic relationships, the sequences of a 389-bp region of the 16s rRNA gene, including variable regions 4 and 5, were compared for 10 strains. These 10 strains formed a single group when their sequences were compared with 16s ribosomal DNA sequences from other species, including Bacteroides spp. from the human colon. On the other hand, the great genetic distances between many P. ruminicola strains, including P. ruminicola subsp. brevis B,4 and GA33 and P. ruminicoh 23T (T = type strain), support the hypothesis that these organisms should be reclassified into new species. We identified signature oligonucleotides based on 16s ribosomal DNA sequences that distinguished strains related to strains 23T, B14, GA33, and M384, as well as an oligonucleotide that specifically recognized all but one of the Bacteroides and Prevotella strains tested. On the basis of the priming activities of these signature oligonucleotides in PCR reactions and on other criteria, we concluded that 12 of the original 29 strains were related to strain 23T, 4 were related to strain B14, and 4 were related to strain GA33. While there are clear grounds for subdividing the species P.ruminicola on the basis of genotypic differences, it is appropriate to delay formal reclassification until further work on the phenotypic differentiation of the new groups is completed.Prevotellu (Bucteroides) ruminicolu has long been recognized as one of the most numerous species inhabiting the rumen (5, 20) and can also account for a high proportion of the hind gut microflora of nonruminants, including pigs and humans (18,30,31). In a recent study, Van Gylswyk (43) found that as many as 60% of bacterial isolates from rumina of silage-fed cows belonged to this species. The new genus Prevotellu was recently created (37) to distinguish certain former Bucteroides species, including Bucteroides ruminicolu, Bucteroides meluninogenicus, and Bucteroides orulis, from the "true" Bucteroides species more closely related to Bucteroides fragilis. P. ruminicolu has generally been regarded as a "widely adapted" species. One potential role of this organism is in the degradation of plant cell wall polysaccharides, such as hemicellulose (7, 47) and pectin (8). P. ruminicolu strains lack a true cellulase system, are not able to degrade crystalline cellulose, and do not cause extensive solubilization of plant cell wall material in pure cultures. On the other hand, there is evidence that these organisms contribute to plant cell wall degradation by acting synergistically with cellulolytic bacteria (28). In addition, P.ruminicolu strains can generally utilize cellodextrins (32), starch (6), and a range of soluble sugars. One of their most significant...

Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut

“…RFLP analyses based on hybridization with 16S rDNA probes have been widely used and depend on detection of variations in chromosomal sequences flanking multiple copies of rRNA target genes (2,28). The approach used here is quite different in that it depends on PCR amplification of internal 16S rDNA fragments and cleavage with restriction enzymes (50).…”

The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract

“…fall into the same phylogenetically diverse group of Gram-negative bacteria as rumen (and human) Prevotella spp. [45], and include both commensal and pathogenic isolates. Several studies have compared full-length or partial sequences of tet(Q) genes carried by rumen P. ruminicola, human oral P. intermedia and human colonic Bacteroides spp.…”

Diversity of Extracellular Proteolytic Activities Among Prevotella Species from the Rumen

“…Anaerobic bacteria are the dominant microbes in rumen contents (up to 10 11 bacteria ml Ϫ1 ) [18] and account for the majority of proteolytic activity in both fluid and particulate matter [17,18]. Further, bacteria are thought to be the primary degraders of soluble protein in the rumen [20].Characterization of the proteolytic activities of individual ruminal bacteria would provide elucidation of the overall process of ruminal protein degradation and allow development of manipulation strategies for bacterial populations.Among bacterial genera in the rumen, Prevotella has been reported to be one of the most numerous [5] and genetically diverse [2,3]. Prevotella spp.…”

“…Among bacterial genera in the rumen, Prevotella has been reported to be one of the most numerous [5] and genetically diverse [2,3]. Prevotella spp.…”