Deoxyribonucleic acid relationships among members of the genus Aeromonas.

Polynucleotide sequences among 24 motile and 11 non-motile aeromonads were studied by analysis of deoxyribonucleic acid - deoxyribonucleic acid (DNA-DNA) duplexes with endonuclease S1. In addition, DNA base composition (mole % guanine and cytosine (G + C)) and relative genome sizes were determined for selected strains. Large variations in genome size were found and % GC ranged from 57.1 to 62.9%. On the basis of the strains examined, the Genus Aeromonas consists of two genotypically legitimate groups: a diverse group of motile aeromonads, and the genetically more homogeneous non-motile aeromonads, comprising the species Aeromonas salmonicida. Internal homology groups could not be demonstrated within the motile aeromonads, and significant divergence in related sequences was indicated. This diverse motile group forms the single species Aeromonas hydrophila.     

Deoxyribonucleic acid base composition of certain species of the genus Bacteroides

The moles percent guanine plus cytosine content of the DNA (% G + C) of 15 Bacteroides strains representing six species was determined. One group, including three strains of Bacteroides ruminicola, two strains of B. melaninogenicus, two strains of B. succinogenes, and one strain of B. oralis (JI), had a % G + C of 47.6--50.3 and a second group including two strains of B. amylophilus, four strains of B. fragilis, and one strain of B. succinogenes had a lower % G + C of 40.3--42.7. The taxonomic relationships among these bacteroides species were discussed.     

Carbohydrate preferences of Bifidobacterium species isolated from the human gut

The growth of nine species of Bifidobacterium on media containing glucose, xylose, xylooligosaccharides (XOS), xylan or fructooligosaccharides (FOS) as the sole carbon source were compared in pure culture. The bifidobacteria differed in fermentation profiles when tested on different carbohydrates. All species grew to their highest final optical density (OD) on a glucose containing medium, with the exception of B. catenulatum which demonstrated a preference for xylose over glucose, and XOS over FOS. B. bifidum grew to the highest OD on XOS compared to xylose suggesting a specific transport system for the oligosaccharide over the monomer. This is consistent with a lack of beta-xylosidase activity present in the culture medium. Lactate, formate and acetate levels were determined and the ratios of these metabolites altered between and within species growing on different carbohydrates. In general, high lactate production correlated with low formate production and low lactate concentrations were obtained at higher levels of formate. Bifidobacteria may alter their metabolic pathways based upon the carbohydrates that are available for their use.     

Deoxyribonucleic acid homologies among strains of Bacteroides melaninogenicus and related species

Saccharolytic, black-pigmented Bacteroides strains, which at present belong to the species Bacteroides melaninogenicus were classified on the basis of deoxyribonucleic acid (DNA) base ratios and DNA hybridization studies. These strains were divided into several DNA homology groups, which showed no or low mutual DNA homology. A DNA homology group with a percentage guanine plus cytosine (G + C) of 42–43% was formed by three strains of Bact. melaninogenicus subsp. melaninogenicus ; the type strain of this subspecies, strain ATCC 25845, had about 60% DNA homology with this group. Strain ATCC 15930, which has been assigned to this subspecies, had a percentage G + C of 47% and showed no DNA homology with the former group. All strains of Bact. melaninogenicus subsp. intermedius had a percentage G + C of 39–45%. A DNA homology group was formed by eight strains of this subspecies. The type strain of Bact. melaninogenicus subsp. intermedius , ATCC 25611, showed relatively low DNA homology with this main DNA homology group. A strain of Bact. melaninogenicus subsp. intermedius serotype C1 showed no DNA homology with the other strains tested. Furthermore two strains labelled 'Bact. melaninogenicus subsp. levii' were found to form a distinct DNA homology group. On the basis of the DNA homology results, the strains, which at present are classified in the species Bact. melaninogenicus , were clearly distinguished from strains of Bact. asaccharolyticus and Bact. gingivalis , and also from strains of related non-pigmented Bacteroides species.     

Immunological relationships among transaldolases in the genus Bifidobacterium

Antisera were prepared against electrophoretically homogeneous transaldolase (dihydroxyacetone transferase, E.C. 2.2.1.2.) of Bifidobacterium thermophilum (B. ruminale) RU326 (ATCC 25866), B. cuniculi RA93 (ATCC 27916) and B. minimum (homology group) F392 (ATCC 27538).Crude extracts of eighty six strains previously assigned to twenty one species of the genus Bifidobacterium on the basis of deoxyribonucleic acid (DNA) homology (DNA-DNA hybridization), were compared by double diffusion tests on Ouchterlony plates. Eight groups of identical antigenic specificity were recognized. By analysis of the spur formation, the groups of identical specificity were arranged in preliminary sequences of decreasing similarity to each of the three homologous transaldolases used as reference point. The relationships between immunological data and the genetic similarity among the species of the genus measured by means of DNA-DNA hybridization were discussed together with some relevant points of bifidal ecology.This investigation was supported by a research grant of Consiglio Nazionale delle Ricerche, Roma.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Four species of the unicellular green alga Chlorella, C. vulgaris, C. luteoviridis, C. minutissima, and C. zofingiensis, were characterized with respect to DNA similarities as determined by quantitative DNA hybridization procedures. In contrast to previous DNA hybridization procedures. In contrast to previous results, C. vulgaris turned out to be a homogeneous species with the exception of strain 211-11c of the Göttingen collection, which was shown to belong to C. kessleri. Similary, C. luteoviridis and C. minutissima represent well defined species in terms of phenotypic and genotypic features. Whitin C. zofingiensis on strain is clearly different with respect to DNA base composition and DNA hybridization data even though it shares phenotypic characteristics with the other strains of C. zofingiensis.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

The genetic relationships of nine strains of Chlorella saccharophila were determined by DNA hybridization techniques. Four strains are closely related to the type strain 211-9a and one strain seems to be moderately related, whereas the taxonomic position of the remaining three strains is not clear. C. saccharophila, like C. sorokiniana, is another species of Chlorella containing strains which are heterogeneous in their overall DNA base sequence and partly also in morphological, biochemical and physiological characters.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

DNA homologies of 14 strains of Chlorella protothecoides were determined. All strains are related by a high degree of DNA similarity (96–102% D) with the exception of strain 211-11 a which proved to belong to C. kessleri. There is, however, no detectable DNA homology with strains of the genus Prototheca which is supposed to have evolved from C. protothecoides by loss of photosynthetic pigments. Even within Prototheca the low degree of DNA similarity indicates a heterogeneity similar to that observed in the genus Chlorella.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

DNA hybridization techniques showed Chlorella fusca var. vacuolata and C. kessleri to be homogeneous species with DNA homologies of 90–100% C. fusca var. fusca and var. rubescens, however, have only about 15% DNA homology with C. fusca var. vacuolata and should no longer be regarded as varieties. A good correlation was found so far between biochemical and physiological characters used in the taxonomy of Chlorella and DNA relatedness. Mutant strains of Chlorella were tested for DNA homologies to prove the reliability of the taxonomical interpretation.     

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.