Background: Kutzneria is a representative of a rarely observed genus of the family Pseudonocardiaceae. Kutzneria species were initially placed in the Streptosporangiaceae genus and later reconsidered ...to be an independent genus of the Pseudonocardiaceae. Kutzneria albida is one of the eight known members of the genus. This strain is a unique producer of the glycosylated polyole macrolide aculeximycin which is active against both bacteria and fungi. Kutzneria albida genome sequencing and analysis allow a deeper understanding of evolution of this genus of Pseudonocardiaceae, provide new insight in the phylogeny of the genus, as well as decipher the hidden secondary metabolic potential of these rare actinobacteria. Results: To explore the biosynthetic potential of Kutzneria albida to its full extent, the complete genome was sequenced. With a size of 9,874,926 bp, coding for 8,822 genes, it stands alongside other Pseudonocardiaceae with large circular genomes. Genome analysis revealed 46 gene clusters potentially encoding secondary metabolite biosynthesis pathways. Two large genomic islands were identified, containing regions most enriched with secondary metabolism gene clusters. Large parts of this secondary metabolism "clustome" are dedicated to siderophores production. Conclusions: Kutzneria albida is the first species of the genus Kutzneria with a completely sequenced genome. Genome sequencing allowed identifying the gene cluster responsible for the biosynthesis of aculeximycin, one of the largest known oligosaccharide-macrolide antibiotics. Moreover, the genome revealed 45 additional putative secondary metabolite gene clusters, suggesting a huge biosynthetic potential, which makes Kutzneria albida a very rich source of natural products. Comparison of the Kutzneria albida genome to genomes of other actinobacteria clearly shows its close relations with Pseudonocardiaceae in line with the taxonomic position of the genus.
To investigate the uptake by the microbial community of easily decomposable exogenous organic C and the proportion of this organic C remaining in soils under long-term fertilization schemes, ...13C-glucose was supplied to arable soils (aquic inceptisol) following a 20-year (1989a2009) application of compost (CM) or inorganic NPK (NPK), along with a control (no fertilizer). Phospholipid fatty acids (PLFAs) were used as biomarkers for actinobacteria, bacteria and fungi. Gas chromatographyacombustionastable isotope ratio mass spectrometry (GCaCaIRMS) was used to determine the incorporation of 13C into individual PLFAs. The concentrations of soil microbial PLFAs significantly (P < 0.05) increased in all three soils after the addition of 13C-glucose. Over a 30-day incubation period, the highest PLFA concentrations were on day 7 (control) or day 15 (NPK and CM) for bacteria, and on day 30 for both fungi and actinobacteria. The added 13C-glucose was incorporated into bacterial PLFAs first, whilst an increase of 13C in fungal and actinobacterial PLFAs was measured on day 7 and 15, respectively. The mean amounts of 13C in bacterial, actinobacterial and fungal PLFAs in CM-treated soil during the 30-day incubation period were 0.589, 0.030 and 0.056 mu g g/1 soil, respectively, which were significantly (P < 0.05) higher than levels measured in the NPK and control soils. Among the bacterial groups, the amount of 13C in Gram-positive (G+) bacteria over the entire incubation ranged from 0.326 to 0.440 mu g g/1 soil in the CM scheme, which was significantly (P < 0.05) higher than levels detected in the NPK and control regimes. In contrast, 13C concentrations in monounsaturated PLFAs (aerobic microorganisms) in the CM-treated soil were 0.030a0.045 mu g g/1 soil, which was significantly (P < 0.05) lower than in the NPK schemes. The proportion of glucose-derived 13C remaining in soils was ranked as follows: CM (53%) > NPK (41%) > control (28%) after 30 days of incubation. Easily decomposable exogenous organic C was thus more effectively maintained under the CM regime, primarily because, after 20 years, CM had altered the microbial community by reducing the ratio of aerobic to anaerobic microorganisms whilst increasing levels of G+ bacteria in soil compared to the control and NPK soils. This study aids our understanding of the transformation and maintenance of easily decomposable organic C in soil over long-term fertilization regimes.
Endophytic actinobacteria, which exist in the inner tissues of living plants, have attracted increasing attention among taxonomists, ecologists, agronomists, chemists and evolutionary biologists. ...Numerous studies have indicated that these prolific actinobacteria appear to have a capacity to produce an impressive array of secondary metabolites exhibiting a wide variety of biological activity, such as antibiotics, antitumor and anti-infection agents, plant growth promoters and enzymes, and may contribute to their host plants by promoting growth and enhancing their ability of withstanding the environmental stresses. These microorganisms may represent an underexplored reservoir of novel species of potential interest in the discovery of novel lead compounds and for exploitation in pharmaceutical, agriculture and industry. This review focuses on new findings in the isolation methods, bio- and chemical diversity of endophytic actinobacteria and reveals the potential biotechnological application. The facing problems and strategies for biodiversity research and bioactive natural products producing are also discussed.
This study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (FBC) process by comparing culturability and ...stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (CTC). The FBC reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. During this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of operation. The plate counts of aerobic chemoorganotrophic bacteria were 3.2-fold higher than CTC-positive (CTC+) counts on average at the fully acclimated stage (after 7 weeks of operation), in which Actinobacteria predominated, as shown by lipoquinone profiling and cultivation methods. When the actinobacterial isolates from the FBC process were grown under aw stress, no significant differences were observed in culturability among the cultures, whereas CTC stainability decreased with reductions in aw levels. A cDNA microarray-based transcriptomic analysis of a representative isolate showed that many of the genes involved in cellular metabolism and genetic information processing were down-regulated by aw stress. This result was fully supported by a proteomic analysis. The results of the present study suggest that, in low aw mature compost, the metabolic activity of the community with Actinobacteria predominating is temporarily reduced to a level that hardly reacts with CTC; however, these bacteria are easily recoverable by exposure to a high aw culture medium. This may be a plausible reason why acclimated FBC reactors in which Actinobacteria predominate yields higher plate counts than CTC+ counts.
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular ...components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea; however, while 'omics can be used ...to infer physiological or ecological roles for species in a community, most of these hypothetical roles remain unvalidated. Here, we report an approach to capture specific microorganisms from complex communities into pure cultures using genome-informed antibody engineering. We apply our reverse genomics approach to isolate and sequence single cells and to cultivate three different species-level lineages of human oral Saccharibacteria (TM7). Using our pure cultures, we show that all three Saccharibacteria species are epibionts of diverse Actinobacteria. We also isolate and cultivate human oral SR1 bacteria, which are members of a lineage of previously uncultured bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life.
Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and ...nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.
Marine sponge-associated microorganisms have proven to be a very promising source of biologically active and pharmaceutically important natural products. In this study, we investigated the diversity ...and antibacterial potential of bacteria from 49 sponge species isolated from the Beibu Gulf, South China Sea, belonging to 16 genera and several unidentified taxa. Using a variety of selective media, 363 strains with different morphologies were identified to six bacterial taxa, including Proteobacteria (α-subgroup 85 and γ-subgroup 59), Actinobacteria (123), Firmicutes (90), Bacteroidetes (5) and Brevundimonas (1). Media ISP2 and R2A were the most effective for isolating Actinobacteria. One hundred and twenty-three actinobacterial strains clustered into 21 genera identified by 16S rDNA gene sequencing, most of which were from the genus Microbacterium, followed by Pseudonocardia, Streptomyces, Kocuria, Aeromicrobium, Brachybacterium and Nocardiopsis, constituted 82% of total actinobacterial isolates. By using the minimal medium, 92 actinobacterial isolates showed antimicrobial activities, and 51 strains displayed moderate to strong antimicrobial activity that inhibited the growth of more than half of the bacteria tested in this study. Functional genes related to secondary metabolites were screened, revealing that 10% (12/123) of actinobacterial isolates contained PKS-KS genes, 18% (22/123) harbored NRPS-A genes and 6% (7/123) had hybrid PKS-NRPS gene clusters. The sponges Haliclona sp., Callyspongia sp. and Desmacella sp., belonging to class Demonspongiae, and Leucaltis sp. from the class Calcarea, were dominant hosts, harboring the most diverse actinobacterial genera with stronger antimicrobial activities and more diverse PKS/NRPS genes.
Actinobacteria is a goldmine for the discovery of abundant secondary metabolites with diverse biological activities. This study explores antimicrobial biosynthetic potential and diversity of ...actinobacteria from Pobitora Wildlife Sanctuary and Kaziranga National Park of Assam, India, lying in the Indo-Burma mega-biodiversity hotspot. A total of 107 actinobacteria were isolated, of which 77 exhibited significant antagonistic activity. 24 isolates tested positive for at least one of the polyketide synthase type I, polyketide synthase type II or non-ribosomal peptide synthase genes within their genome. Their secondary metabolite pathway products were predicted to be involved in the production of ansamycin, benzoisochromanequinone, streptogramin using DoBISCUIT database. Molecular identification indicated that these actinobacteria predominantly belonged to genus Streptomyces, followed by Nocardia and Kribbella. 4 strains, viz. Streptomyces sp. PB-79 (GenBank accession no. KU901725; 1313 bp), Streptomyces sp. Kz-28 (GenBank accession no. KY000534; 1378 bp), Streptomyces sp. Kz-32 (GenBank accession no. KY000536; 1377 bp) and Streptomyces sp. Kz-67 (GenBank accession no. KY000540; 1383 bp) showed ~89.5% similarity to the nearest type strain in EzTaxon database and may be considered novel. Streptomyces sp. Kz-24 (GenBank accession no. KY000533; 1367 bp) showed only 96.2% sequence similarity to S. malaysiensis and exhibited minimum inhibitory concentration of 0.024 µg/mL against methicilin resistant Staphylococcus aureus ATCC 43300 and Candida albicans MTCC 227. This study establishes that actinobacteria isolated from the poorly explored Indo-Burma mega-biodiversity hotspot may be an extremely rich reservoir for production of biologically active compounds for human welfare.
Saccharibacteria (TM7) are obligate epibionts living on the surface of their host bacteria and are strongly correlated with dysbiotic microbiomes during periodontitis and other inflammatory diseases, ...suggesting they are putative pathogens. However, due to the recalcitrance of TM7 cultivation, causal research to investigate their role in inflammatory diseases is lacking. Here, we isolated multiple TM7 species on their host bacteria from periodontitis patients. These TM7 species reduce inflammation and consequential bone loss by modulating host bacterial pathogenicity in a mouse ligature-induced periodontitis model. Two host bacterial functions involved in collagen binding and utilization of eukaryotic sialic acid are required for inducing bone loss and are altered by TM7 association. This TM7-mediated downregulation of host bacterial pathogenicity is shown for multiple TM7/host bacteria pairs, suggesting that, in contrast to their suspected pathogenic role, TM7 could protect mammalian hosts from inflammatory damage induced by their host bacteria.
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•Saccharibacteria (TM7) is an epibiont that lives on the surface of Actinobacteria•Multiple TM7 isolates from periodontitis patients decrease inflammatory bone loss•TM7 reduce bone loss by modulating the pathogenicity of their host Actinobacteria•TM7 could serve a protective role for mammalian hosts in inflammatory diseases
If certain bacteria are increased in disease, does that mean they are bad? Chipashvili et al. show that this may not be the case for ultrasmall Saccharibacteria. By using a mouse model for periodontitis, they determined that Saccharibacteria offer protection by reducing the pathogenicity of other bacteria in inflammatory diseases.
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