16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species).

The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.

Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium.

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13(T), isolated from a rain water pond at a plant nursery in Spain and characterized as a plant-growth-promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15-40 °C, at pH 5.0-8.

Description of Streptomonospora sediminis sp. nov. and Streptomonospora nanhaiensis sp. nov., and reclassification of Nocardiopsis arabia Hozzein & Goodfellow 2008 as Streptomonospora arabica comb. nov. and emended description of the genus Streptomonospora.

Two actinomycete strains isolated from marine sediment samples, designated YIM M11335(T) (from the Indian Ocean) and 12A09(T) (from the South China Sea), were obtained and examined by a polyphasic approach. The two Gram-staining-positive, aerobic strains produced branched substrate mycelia and aerial hyphae that were not fragmented, and no diffusible pigment was produced on the media tested. At maturity, spore chains and single spores were formed on aerial hyphae and substrate mycelium, respectively.

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant.

Two actinobacterial strains, CPCC 203464(T) and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements.

Actinopolyspora righensis sp. nov., a novel halophilic actinomycete isolated from Saharan soil in Algeria.

A novel halophilic actinomycete strain, H23(T), was isolated from a Saharan soil sample collected in Djamâa (Oued Righ region), El-Oued province, South Algeria. Strain H23(T) was identified as a member of the genus Actinopolyspora by a polyphasic approach. Phylogenetic analysis showed that strain H23(T) had 16S rRNA gene sequence similarities ranging from 97.

opm: an R package for analysing OmniLog(R) phenotype microarray data.

Summary: opm is an R package designed to analyse multidimensional OmniLog® phenotype microarray (PM) data. opm provides management, visualization and statistical analysis of PM data, including curve-parameter estimation and discretization, dedicated and customizable plots, metadata management, automated generation of textual and tabular reports, mapping of substrates to databases, batch conversion of files and export to phylogenetic software in the YAML markup language.

Availability: opm is distributed under the GPL through the Comprehensive R Archive Network (http://cran.

Geodermatophilus africanus sp. nov., a halotolerant actinomycete isolated from Saharan desert sand.

A novel Gram-strain positive, aerobic, actinobacterial strain, designated CF11/1(T), was isolated from a sand sample obtained in the Sahara Desert, Chad. The black-pigmented isolate was aerobic and exhibited optimal growth from 25 to 35 °C at pH 6.0-8.

Actinopolyspora mzabensis sp. nov., a halophilic actinomycete isolated from an Algerian Saharan soil.

A halophilic actinomycete strain, designated H55(T), was isolated from Saharan soil sampled in the Mzab region (Ghardaïa, southern Algeria) and was characterized in a taxonomic study using a polyphasic approach. The cell wall was determined to contain meso-diaminopimelic acid and the characteristic whole-cell sugars were arabinose and galactose. The predominant menaquinones were found to be MK-10(H4) and MK-9(H4).

Microlunatus cavernae sp. nov., a novel actinobacterium isolated from Alu ancient cave, Yunnan, South-West China.

A Gram-positive, coccoid, non-endospore-forming actinobacterium, designated YIM C01117(T), was isolated from a soil sample collected from Alu ancient cave, Yunnan province, south-west China. Based on the 16S rRNA gene sequence analysis, strain YIM C01117(T) was shown to belong to the genus Microlunatus, with highest sequence similarity of 97.4 % to Microlunatus soli DSM 21800(T).

Saccharothrix saharensis sp. nov., an actinomycete isolated from Algerian Saharan soil.

The taxonomic position of a novel actinomycete, strain SA152(T), isolated from a sample of Algerian Saharan soil, was determined using a polyphasic taxonomic approach. The strain produced abundant aerial mycelium and fragmented substrate mycelium on most media tested. Chemotaxonomically and phylogenetically, the strain was related to the members of the genus Saccharothrix.

Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.

The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N.

When should a DDH experiment be mandatory in microbial taxonomy?

DNA-DNA hybridizations (DDH) play a key role in microbial species discrimination in cases when 16S rRNA gene sequence similarities are 97 % or higher. Using real-world 16S rRNA gene sequences and DDH data, we here re-investigate whether or not, and in which situations, this threshold value might be too conservative. Statistical estimates of these thresholds are calculated in general as well as more specifically for a number of phyla that are frequently subjected to DDH.

Geodermatophilus normandii sp. nov., isolated from Saharan desert sand.

A novel Gram-reaction-positive actinobacterial strain, designated CF5/3(T), was isolated from a sand sample obtained in the Sahara Desert, Chad. The greenish-black-pigmented isolate was aerobic and exhibited optimal growth from 25-40 °C at pH 6.0-10.

Kribbella shirazensis sp. nov., isolated from Iranian soil.

The taxonomic position of a strain isolated from soil in Shiraz, Fars province, Iran, was investigated. Strain UTMC 693(T) produced an extensively branched substrate mycelium and aerial hyphae consisting of hyphae that fragment into short to elongated rod-like elements. The chemotaxonomic characteristics of the isolate matched those described for the genus Kribbella.

Blastococcus endophyticus sp. nov., an actinobacterium isolated from Camptotheca acuminata.

A novel endophytic actinobacterium, designated strain YIM 68236(T), was isolated from healthy leaves of Camptotheca acuminata. and characterized by using a polyphasic approach. Cells of this strain occurred singly, in pairs or in tetrads.

Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)).

Owenweeksia hongkongensis Lau et al. 2005 is the sole member of the monospecific genus Owenweeksia in the family Cryomorphaceae, a poorly characterized family at the genome level thus far. This family comprises seven genera within the class Flavobacteria.

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).

Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G.

Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)).

Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order 'Rhizobiales', which is thus far poorly characterized at the genome level. Cultures from this species are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it.

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13.

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S.

Diversity of Termitomyces associated with fungus-farming termites assessed by cultural and culture-independent methods.

Background: Fungus-cultivating termites make use of an obligate mutualism with fungi from the genus Termitomyces, which are acquired through either vertical transmission via reproductive alates or horizontally transmitted during the formation of new mounds. Termitomyces taxonomy, and thus estimating diversity and host specificity of these fungi, is challenging because fruiting bodies are rarely found. Molecular techniques can be applied but need not necessarily yield the same outcome than morphological identification.

Genome sequence-based species delimitation with confidence intervals and improved distance functions.

Background: For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes.

Geodermatophilus tzadiensis sp. nov., a UV radiation-resistant bacterium isolated from sand of the Saharan desert.

Three novel Gram-positive, aerobic, actinobacterial strains, CF5/2(T), CF5/1 and CF7/1, were isolated in 2007 during environmental screening of arid desert soil in the Sahara desert, Chad. Results from riboprinting, MALDI-TOF protein spectra and 16S rRNA sequence analysis confirmed that all three strains belonged to the same species. Phylogenetic analysis of 16S rRNA sequences with the strains' closest relatives indicated that they represented a distinct species.

Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names.

High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).

Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D.

Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).

Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N.