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PubMed2004

The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes.

Fibrobacteres, Chlorobi, and Bacteroidetes (FCB group) comprise three main bacterial phyla recognized on the basis of 16S rRNA trees. Presently, there are no distinctive biochemical or molecular characteristics known that can distinguish these bacteria from other bacterial phyla. The relationship of these bacteria to other phyla is also not known. This review describes many signatures, consisting of defined and conserved inserts in widely distributed proteins, that provide distinctive molecular markers for these groups of bacteria. These signatures serve to clarify the evolutionary relationship between members of the FCB group, and to other bacterial phyla. A 4 aa insert in DNA Gyrase B (GyrB) and a 45 aa insert in the SecA proteins are uniquely shared by various Bacteroidetes species. The insert in GyrB is present in all Bacteroidetes species (>100) covering different orders and families, indicating that it is a distinctive characteristic of the group. Three signatures consisting of an 18 aa insert in ATPase alpha-subunit, an 8-9 aa insert in the FtsK protein and a 1 aa insert in the UvrB protein are commonly shared only by the Bacteroidetes and Chlorobi homologs providing evidence that these two groups are specifically related to each other. Two additional inserts in the RNA polymerase beta'-subunit (5-7 aa) and Serine hydroxymethyl-transferase (14-16 aa), which are commonly present in various Bacteroidetes, Chlorobi, and Fibrobacteres homologs, but not any other bacteria, provide evidence that these groups shared a common ancestor exclusive of all other bacteria. The FCB groups of bacteria are indicated to have diverged from this common ancestor in the following order: Fibrobacteres --> Chlorobi --> Bacteriodetes. The inferences from signature sequences are strongly supported by phylogenetic analyses. These observations suggest that the FCB groups of bacteria should be placed in a single phylum rather than three distinct phyla. Signature sequences in a number of other proteins provide evidence that the FCB group of bacteria diverged at a similar time as the Chlamydiae group, and that the Spirochetes and Aquificales groups are its closest relatives.

Adenosine Triphosphatases↗
PubMed2006

Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea.

The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea; depth: 50 and 2000 m) and Mediterranean (Ionian Sea; depth 50 and 3000 m) waters were studied by PCR amplification and sequencing of the last 450-500 bp of the 16S rRNA gene. A total of 1621 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated with geographical location and depth. The Ionian 50 m sample appeared to be the most diverse and also had remarkable differences in terms of the prokaryotic groups retrieved; surprisingly, however, many similarities were found at the level of large-scale diversity between the Sargasso database fragments and the Greenland 50 m sample. Most sequences with more than 97% sequence similarity, a value often taken as indicative of species delimitation, were only found at a single location/depth; nevertheless, a few examples of cosmopolitan sequences were found in all samples. Depth was also an important factor and, although both deep-water samples had overall similarities, there were important differences that could be due to the warmer waters at depth of the Mediterranean Sea.

Archaea↗
PubMed1963

Incorporation of isobutyrate and valerate into cellular plasmalogen by Bacteroides succinogenes.

Wegner, G. H. (University of Wisconsin, Madison) and E. M. Foster. Incorporation of isobutyrate and valerate into cellular plasmalogen by Bacteroides succinogenes. J. Bacteriol. 85:53-61. 1963.-Bacteroides succinogenes was found to require both a branched-chain volatile fatty acid (e.g., isobutyric) and a straight-chain acid (e.g., valeric) for growth. The organism used the acids as precursors for the synthesis of long-chain fatty acids and fatty aldehydes, which in turn were employed in the synthesis of phospholipid, mainly ethanolamine plasmalogen. Isobutyric acid was incorporated primarily into branched-chain C(14) and C(16) acids (tentatively identified as 12-methyl tridecanoic and 14-methyl pentadecanoic acids, respectively), and into fatty aldehydes. Valeric acid was used mainly for the synthesis of n-C(13) and n-C(15) fatty acids and fatty aldehydes. Apparently the two short-chain fatty acids were built up by the addition of two-carbon units to form the long-chain acids and aldehydes of the plasmalogen.

Aldehydes↗
PubMed1965

VITAMIN REQUIREMENTS OF SEVERAL CELLULOLYTIC RUMEN BACTERIA.

Scott, H. W. (Ohio Agricultural Experiment Station, Wooster), and B. A. Dehority. Vitamin requirements of several cellulolytic rumen bacteria. J. Bacteriol. 89:1169-1175. 1965.-Four strains of cellulolytic bacteria recently isolated from in vitro rumen fermentations were used in this study. Nine water-soluble vitamins were tested in single-deletion and single-addition plus biotin experiments, each with and without charcoal-extracted casein hydrolysate. Bacteroides succinogenes A3C and B21a required only biotin under the above experimental conditions. Ruminococcus flavefaciens B34b showed an absolute requirement for biotin and was stimulated by p-aminobenzoic acid (PABA) in the single-deletion experiments. In the single-addition plus biotin experiments, PABA and, to a lesser extent, vitamin B(12) appeared to be required for maximal growth. The presence or absence of casein hydrolysate did not affect the vitamin requirements for the aforementioned three strains. In the single-deletion experiments, R. flavefaciens Cla showed an absolute requirement for biotin and, when casein hydrolysate was omitted, for B(12). When casein hydrolysate was present, no requirement for B(12) could be observed. In the single-addition experiments where the basal medium contained biotin and casein hydrolysate or B(12), PABA was required for maximal growth; however, the single deletion of PABA caused only slight retardation of growth. Investigation of the B(12) or casein hydrolysate requirement of Cla revealed that a mixture of purified amino acids simulating casein hydrolysate satisfied this requirement. Subsequent work indicated that this requirement could be satisfied by the amino acid methionine.

4-Aminobenzoic Acid↗
PubMed1965

DEGRADATION AND UTILIZATION OF ISOLATED HEMICELLULOSE BY PURE CULTURES OF CELLULOLYTIC RUMEN BACTERIA.

Dehority, B. A. (Ohio Agricultural Experiment Station, Wooster). Degradation and utilization of isolated hemicellulose by pure cultures of cellulolytic rumen bacteria. J. Bacteriol. 89:1515-1520. 1965.-Hemicelluloses isolated from flax, corn hulls, alfalfa, oat hulls, and fescue grass were used as sole energy sources to study the ability of pure cultures of cellulolytic rumen bacteria to degrade and utilize these materials. From a total of eight bacterial strains tested (three strains of Bacteroides succinogenes, four strains of Ruminococcus flavefaciens, and one strain of Ruminococcus albus), only three strains of ruminococci were able to utilize the hemicelluloses for growth. Hemicellulose fermentation mixtures were analyzed for total pentose, residual hemicellulose (pentose precipitated in 80% ethyl alcohol), and ethyl alcohol-soluble pentose. The three strains of ruminococci were able to partially utilize the different hemicelluloses as energy sources, as determined by total pentose loss, and they were capable of almost complete degradation of the original hemicellulose from an ethyl alcohol-insoluble to ethyl alcohol-soluble form. The extent of both degradation and utilization varied markedly between the three strains and different substrates. Tests on the other strains indicated that no growth, production of organic acid end products, or appreciable loss of total pentose had occurred. However, analysis of the culture medium for residual hemicellulose indicated that these strains were able to extensively degrade the original hemicelluloses to an ethyl alcohol-soluble form. Marked differences were observed among strains and hemicelluloses in the amount of hemicellulose degraded. Of the different hemicelluloses, corn-hull hemicellulose was the most resistant to degradation and utilization by the cellulolytic rumen bacteria.

Animals↗
PubMed2026

Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.

BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem. RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways. CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.

Multiomics↗