Biomedical subjects

Matthew D Collins

Publications and source records attributed to Matthew D Collins.

60 records · Page 4Linked to original sources

PubMed2002

Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs.

In spite of its shortcoming, analysis of PCR-derived rDNA libraries is being employed increasingly to investigate microbial diversity within many ecosystems. In the present investigation, the effects of the number of PCR cycles (10 vs 25 cycles) on the inferred structure of a 16S rDNA library have been examined. Seventy-five 25-cycle sequences were retrieved and analysed in comparison with 284 10-cycle sequences already described in a previous study. The 359 clones obtained were classified into 94 molecular species (at least 98% sequence similarity). At the level of large phylogenetic groups, the two cloned rDNA libraries were not different. A mathematical model was developed in order to estimate the number of molecular species expected if further sequencing was performed. Coverage-based computing, projections and statistical analysis demonstrated that the structures of the two PCR-derived rDNA libraries were different and that the 25-cycle rDNA library displayed reduced diversity. It is suggested that the number of PCR cycles used for amplification of 16S rDNA genes for phylogenetic diversity studies must therefore be kept as small as possible.

Adult↗

PubMed2002

Bifidobacterium scardovii sp. nov., from human sources.

Five strains of an unusual catalase-negative Gram-positive asporogenous rod-shaped bacterium from human sources were subjected to a polyphasic taxonomic study. The presence of fructose-6-phosphate phosphoketolase, a key enzyme of bifidobacterial hexose metabolism, indicated the strains were members of the genus Bifidobacterium but they did not correspond to any of the recognized species of this genus on the basis of biochemical profiles and whole-cell protein analyses. Comparative 16S rRNA gene sequencing confirmed the placement of the isolates in the genus Bifidobacterium, and demonstrated they represent a hitherto unknown subline within the genus displaying > 5% sequence divergence with recognized species. Based on both phenotypic and phylogenetic criteria, it is proposed that the isolates recovered from human sources be classified as a new species, Bifidobacterium scardovii sp. nov.; the type strain is CCUG 13008T (= DSM 13734T).

Adult↗

PubMed2002

Nesterenkonia lacusekhoensis sp. nov., isolated from hypersaline Ekho Lake, East Antarctica, and emended description of the genus Nesterenkonia.

An aerobic and heterotrophic isolate, designated IFAM EL-30T, was obtained from hypersaline Ekho Lake (Vestfold Hills, East Antarctica). The isolate consisted of Gram-positive cocci or short rods which occasionally exhibited branching. The organism was moderately halotolerant, required thiamin.HCI and was stimulated by biotin and nicotinic acid. It grew well with glucose, acetate, pyruvate, succinate, malate or glutamate, and hydrolysed DNA but not gelatin, starch or Tween 80. Nitrate was aerobically reduced to nitrite. Chemical analysis revealed diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid as the major polar lipids. The cellular fatty acids were predominantly of the anteiso and iso methyl-branched types, and the major menaquinone6 were MK-7 and MK-8. The peptidoglycan type was A4alpha, L-Lys-L-Glu. The DNA base ratio was 66.1 mol% G+C. Comparisons of 16S rRNA gene sequences showed that the unidentified organism was phylogenetically closely related to Nesterenkonia halobia, although a sequence divergence value of > 3% demonstrated that the organism represents a different species. On the basis of phenotypic and genotypic evidence, it is proposed that the unknown bacterium be designated as a new species of the genus Nesterenkonia, namely Nesterenkonia lacusekhoensis sp. nov., the type strain being IFAM EL-30T (= DSM 12544T = CIP 107030T). An emended description of the genus Nesterenkonia is given.

Antarctic Regions↗

PubMed2002

Streptococcus gallinaceus sp. nov., from chickens.

Three isolates of an unknown Gram-positive, catalase-negative, chain-forming, coccus-shaped organism isolated from an outbreak of septicaemia in a flock of adult broiler parents were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the bacterium represents a new subline within the genus Streptococcus, related to, albeit distinct from, Streptococcus acidominimus, Streptococcus ovis, Streptococcus suis and close relatives. The unknown bacterium was readily distinguished from all recognized streptococcal species by biochemical tests. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from chickens be classified as Streptococcus gallinaceus sp. nov. The type strain is CCUG 42692T (= CIP 107087T).

Animals↗

PubMed2002

Actinomyces coleocanis sp. nov., from the vagina of a dog.

A hitherto undescribed Actinomyces-like bacterium was isolated from the vagina of a dog. Biochemical testing and PAGE analysis of whole-cell proteins indicated that the isolate was phenotypically different from previously described Actinomyces species and related taxa. Sequencing of 165 rRNA showed that the unknown bacterium was distinct from all currently known Actinomyces species. Phylogenetically, the unidentified organism displayed a specific association with Actinomyces europaeus, but a sequence divergence of > 5% demonstrated that it represents a distinct species. Based on both phenotypic and 165 rRNA sequence considerations, it is proposed that the unknown strain from a dog be classified as a novel species, Actinomyces coleocanis sp. nov. The type strain is CCUG 41708T (= CIP 106873T).

Actinomyces↗

PubMed2002

Phylogenetic, amino acid content and indel analyses of the beta subunit of DNA-dependent RNA polymerase of gram-positive and gram-negative bacteria.

In this study, we have sequenced the rpoB gene, encoding the beta subunit of DNA-dependent RNA polymerase, from a selection of gram-positive and gram-negative bacteria. The presence of insertions and deletions (indels) in the beta subunit separate the gram-positive and gram-negative bacteria from each other and support the division of the gram-positive organisms into two clades based on DNA G+C content. Phylogenetic and amino acid content analyses further separate the clostridia from bacilli, leuconostocs, listeriae and relatives, forming an early branch after the common gram-positive ancestor. The occurrence in the beta subunit of Asn-Ala at positions 471-472 in Porphyromonas cangingivalis and Asn at position 372 in Weissella paramesenteroides are postulated to be the cause of the natural rifampicin resistance of these species.

Amino Acid Sequence↗