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1.
Syst Appl Microbiol ; 38(7): 472-82, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26283320

ABSTRACT

Recent developments in sequencing technology have given rise to a large number of studies that assess bacterial diversity and community structure in termite and cockroach guts based on large amplicon libraries of 16S rRNA genes. Although these studies have revealed important ecological and evolutionary patterns in the gut microbiota, classification of the short sequence reads is limited by the taxonomic depth and resolution of the reference databases used in the respective studies. Here, we present a curated reference database for accurate taxonomic analysis of the bacterial gut microbiota of dictyopteran insects. The Dictyopteran gut microbiota reference Database (DictDb) is based on the Silva database but was significantly expanded by the addition of clones from 11 mostly unexplored termite and cockroach groups, which increased the inventory of bacterial sequences from dictyopteran guts by 26%. The taxonomic depth and resolution of DictDb was significantly improved by a general revision of the taxonomic guide tree for all important lineages, including a detailed phylogenetic analysis of the Treponema and Alistipes complexes, the Fibrobacteres, and the TG3 phylum. The performance of this first documented version of DictDb (v. 3.0) using the revised taxonomic guide tree in the classification of short-read libraries obtained from termites and cockroaches was highly superior to that of the current Silva and RDP databases. DictDb uses an informative nomenclature that is consistent with the literature also for clades of uncultured bacteria and provides an invaluable tool for anyone exploring the gut community structure of termites and cockroaches.


Subject(s)
Bacteria/classification , Bacteria/genetics , Cockroaches/microbiology , Gastrointestinal Microbiome , Isoptera/microbiology , Animals , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , High-Throughput Nucleotide Sequencing , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
2.
Antonie Van Leeuwenhoek ; 107(5): 1127-34, 2015 May.
Article in English | MEDLINE | ID: mdl-25663029

ABSTRACT

An actinobacterial strain, MV32(T), was isolated from the paunch region of the hindgut of a South African termite, Amitermes hastatus, as part of an investigation of the actinobacterial population residing within this higher order termite species. Strain MV32(T) was chosen for further study from amongst the many potentially novel actinomycete isolates because of its strong antibacterial activity against Mycobacterium aurum A+. 16S rRNA gene phylogenetic analyses clearly placed strain MV32(T) within the genus Streptomyces, with 99.3% sequence similarity to its closest relative, Streptomyces endophyticus YIM 65594(T). Despite this high sequence similarity, DNA-DNA hybridisation analysis showed a DNA relatedness value of 62 ± 2%, to S. endophyticus DSM 41984(T) (indicating that strain MV32(T) belongs to a different genomic species), as well as values of 14.4 ± 0.8 and 10.4 ± 2.9%, respectively, to its next closest relatives, Streptomyces kunmingensis NRRL B-16240(T) and Streptomyces cinnabarinus NRRL B-12382(T). Based on these results and supported by both chemotaxonomic data and a number of phenotypic differences, strain MV32(T) is proposed to represent a new species within the genus Streptomyces, with the name Streptomyces fractus (= DSM 42163(T) = NRRL B-59159(T)).


Subject(s)
Isoptera/microbiology , Streptomyces/classification , Streptomyces/isolation & purification , Animals , Bacterial Typing Techniques , DNA, Bacterial/genetics , Gastrointestinal Tract/microbiology , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , South Africa , Streptomyces/genetics
3.
J Antibiot (Tokyo) ; 67(12): 813-8, 2014 Dec.
Article in English | MEDLINE | ID: mdl-24961711

ABSTRACT

Two novel members of the genus Amycolatopsis were isolated from soil samples collected in South Africa. Strains JS72(T) and M29(T) clustered in the same clade in the 16S-rRNA, gyrB-16S-rRNA and gyrB-recN gene trees. Both strains showed anti-mycobacterial activity. The oxyB P450 monooxygenase B gene required for the production of glycopeptide antibiotics was detected in both strains, while strain JS72(T) was also shown to contain the 3-amino-5-hydroxy-benzoic acid synthase gene, which is required for the production of the ansamycin class of antibiotics. Genetic distance values (based on the gyrB and recN genes) were calculated between strains JS72(T) and M29(T) and their closest phylogenetic relatives. The values for strain JS72(T) were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis-type strains. The gyrB-based values for strain M29(T) were above the threshold for all but one strain; the recN-based values were all above the threshold. These data, along with DNA-DNA hybridization data, showed that strains JS72(T) and M29(T) belong to distinct genomic species. The physiological, phylogenetic and genetic distance data support the description of strains JS72(T) and M29(T) as the type strains of novel species, for which the names Amycolatopsis speibonae sp. nov. (=DSM 46660(T)=NRRL B-24958(T)) and Amycolatopsis roodepoortensis sp. nov. (=DSM 46661(T)=NRRL B-24959(T)) are proposed, respectively.


Subject(s)
Actinomycetales/chemistry , Actinomycetales/isolation & purification , Anti-Bacterial Agents/biosynthesis , Anti-Bacterial Agents/isolation & purification , Soil Microbiology , Actinomycetales/genetics , Actinomycetales/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Base Sequence , DNA Gyrase/chemistry , DNA Gyrase/genetics , DNA Restriction Enzymes/chemistry , DNA Restriction Enzymes/genetics , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Microbial Sensitivity Tests , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Alignment , Sequence Analysis, DNA , South Africa
4.
Antonie Van Leeuwenhoek ; 100(4): 589-605, 2011 Nov.
Article in English | MEDLINE | ID: mdl-21720857

ABSTRACT

A multi-faceted screening programme was designed to search for the oxidases, laccase, peroxidase and tyrosinase. Actinobacteria were selectively isolated from the paunch and colon region of the hindguts of the higher termite, Amitermes hastatus. The isolates were subjected to solid media assays (dye decolourization, melanin production and the utilization of indulin AT as sole carbon source) and liquid media assays. Eleven of the 39 strains had the ability to decolourize the dye RBBR, an indicator for the production of peroxidases in actinobacteria. Melanin production on ISP6 and ISP7 agar plates served as a good indicator for laccase and/or tyrosinase production and the ability of the strains to grow in the presence of indulin AT as a sole carbon source served as a good indicator of lignin peroxidase and/or general peroxidase production. Enzyme-producing strains were cultivated in liquid media and extracellular enzyme activities measured. Strains with the ability to produce oxidative enzymes under the conditions tested were identified to genus level by 16S rRNA gene analysis and compared to known oxidase producers. A strong relationship was observed between the environment sampled (termite guts where lignocellulose degradation occurs) and the dominant type of oxidative enzyme activity detected (laccases and peroxidases), which suggests the possibility of future targeted screening protocols linking the physical properties of the target enzymes with specific operational conditions required, such as lignocellulosic degradation in the preparation of biofuel feedstocks.


Subject(s)
Actinobacteria/enzymology , Bacterial Proteins/metabolism , Isoptera/microbiology , Oxidoreductases/metabolism , Actinobacteria/classification , Actinobacteria/genetics , Actinobacteria/isolation & purification , Animals , Bacterial Proteins/genetics , Gastrointestinal Tract/metabolism , Gastrointestinal Tract/microbiology , Isoptera/metabolism , Lignin/metabolism , Molecular Sequence Data , Oxidoreductases/genetics , Phylogeny
5.
Int J Syst Evol Microbiol ; 59(Pt 8): 2032-5, 2009 Aug.
Article in English | MEDLINE | ID: mdl-19567563

ABSTRACT

As part of an enzyme-screening programme, an actinobacterium, strain HSM#10T, was isolated from a sample collected from the base of a translucent quartz rock in Miers Valley, eastern Antarctica. The isolate produced branching vegetative mycelium that was characteristic of filamentous actinobacteria. The chemotaxonomic characteristics of the strain suggested that HSM#10T should be classified as a member of the genus Streptomyces. Furthermore, phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to members of the genus Streptomyces, which supports the classification of this strain within the family Streptomycetaceae. Phenotypic and phylogenetic results allowed strain HSM#10T to be differentiated from known streptomycetes. DNA-DNA hybridization data also showed that strain HSM#10T could be differentiated from its nearest phylogenetic neighbours Streptomyces chryseus DSM 40420T (53.55+/-3.15% DNA relatedness), Streptomyces helvaticus DSM 40431T (38.75+/-2.75%), Streptomyces flavidovirens DSM 40150T (30.7+/-2.90%) and Streptomyces albidochromogenes DSM 41800T (33.9+/-0.10%). Therefore, the name Streptomyces hypolithicus sp. nov. is proposed, with HSM#10T (=DSM 41950T=NRRL B-24669T) as the type strain.


Subject(s)
Soil Microbiology , Streptomyces/classification , Streptomyces/isolation & purification , Antarctic Regions , Bacterial Typing Techniques , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Microscopy, Electron, Scanning , Molecular Sequence Data , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Streptomyces/genetics , Streptomyces/physiology
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