Beutenbergia cavernae gen. nov., sp. nov., an L-lysine-containing actinomycete isolated from a cave

Diversity, Ecology, and Prevalence of Antimicrobials in Nature

Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.

Cave Actinobacteria as Producers of Bioactive Metabolites

Recently, there is an urgent need for new drugs due to the emergence of drug resistant pathogenic microorganisms and new infectious diseases. Members of phylum Actinobacteria are promising source of bioactive compounds notably antibiotics. The search for such new compounds has shifted to extreme or underexplored environments to increase the possibility of discovery. Cave ecosystems have attracted interest of the research community because of their unique characteristics and the microbiome residing inside including actinobacteria. At the time of writing, 47 species in 30 genera of actinobacteria were reported from cave and cave related habitats. Novel and promising bioactive compounds have been isolated and characterized. This mini-review focuses on the diversity of cultivable actinobacteria in cave and cave-related environments, and their bioactive metabolites from 1999 to 2018.

Litorihabitans aurantiacus gen. nov., sp. nov., an actinobacterium of the family Beutenbergiaceae isolated from beach sand

A novel actinobacterium, designated HIsM16-52^T, was isolated from beach sand collected from Ishigaki Island in Japan and its taxonomic position was investigated by a polyphasic approach. Strain HIsM16-52^T contained both lysine and ornithine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and C14 : 0. The detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was determined to be 73.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIsM16-52^T fell within the cluster of the family Beutenbergiaceae and formed a reliable cluster with the members of the genus Serinibacter. The highest 16S rRNA gene sequence similarities were obtained to species of the genus Serinibacter(97.8-97.9 %), followed by the genera Miniimonas (97.0 %), Beutenbergia (96.4 %) and Salana (95.9 %). However, strain HIsM16-52^T differed from the members of the genus Serinibacter and the other genera within the family Beutenbergiaceae in terms of chemotaxonomic characteristics. Therefore, strain HIsM16-52^T is concluded to represent a novel genus and species of the family Beutenbergiaceae, for which the name Litorihabitans aurantiacus gen. nov., sp. nov. is proposed. The type strain of L. aurantiacus is HIsM16-52^T (=NBRC 112290^T=TBRC 7759^T).

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

Actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. Cave ecosystems are unusual and rarely studied. Here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in Siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of one active strain. Streptomyces genera isolates from moonmilk speleothem demonstrated antibacterial and antifungal activities. Some of the strains were able to inhibit the growth of pathogenic Candida albicans.

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems.

Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity

Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.

Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation

Traditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters. Lactobacillales and Saccharomycetales dominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistant Bacillales, Eurotiales, and Mucorales were considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation. Enterobacteriales were consistently ubiquitous throughout the process. For the cellulolytic communities, only the genera Sanguibacter, Beutenbergia, Agrobacterium, and Erwinia dominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance of Bacillus, Aspergillus, and Mucor. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, β-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters.

Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India) and their antimicrobial activities

Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups), Micromonospora (4), Amycolatopsis (3), Arthrobacter (3), Kitasatospora (2), Janibacter (1), Nocardia (1), Pseudonocardia (1) and Rhodococcus (1). Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS). The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

Streptomyces canchipurensis sp. nov., isolated from a limestone habitat

Hundung Limestone habitat, Manipur, India is an unexplored site for microbial diversity studies. Using polyphasic taxonomy, a Streptomyces strain, MBRL 172(T), has been characterized. The strain was found to show highest 16S rRNA gene sequence similarity with Streptomyces coeruleofuscus NBRC 12757(T) (99.2 %). The DNA relatedness between MBRL 172(T) and S. coeruleofuscus NBRC 12757(T), and between MBRL 172(T) and Streptomyces nogalater NBRC 13445(T), were 36.8 ± 4.4 and 52.5 ± 2.7 %, respectively. Strain MBRL 172(T) was found to contain LL-diaminopimelic acid as the diagnostic diamino acid and glucose, mannose and xylose as the major sugars in whole cell hydrolysates. The polar lipids in the cell membrane were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositolmannoside. The predominant menaquinones detected were MK-9(H6) and MK-9(H8). The cellular fatty acids identified were mainly saturated fatty acids: anteiso-C15:0, iso-C16:0 and iso-C15:0. Based on differences in the biochemical and molecular characteristics from its closest relatives, the strain can be proposed to represent a novel taxon in the genus Streptomyces, for which the name Streptomyces canchipurensis is proposed, with the type strain MBRL 172(T) (=JCM 17575(T) = KCTC 29105(T)).

Diversity and isolation of rare actinomycetes: an overview

A renewed interest in the development of new antimicrobial agents is urgently needed to combat the increasing number of antibiotic-resistant strains of pathogenic microorganisms. Actinomycetes continue to be the mainstream supplier of antibiotics used in industry. The likelihood of discovering a new compound with novel chemical structure can be increased with intensive efforts in isolating and screening of rare genera of microorganisms to include in natural-product-screening collections. An unexpected variety of rare actinomycetes is now being isolated worldwide from previously uninvestigated diverse natural habitats, using different selective isolation methods. These isolation efforts include methods to enhance growth (enrichment) of rare actinomycetes, and eliminate unwanted microorganisms (pretreatment). To speed up the strain isolation process, knowledge about the distribution of such unexploited groups of microorganisms must also be augmented. This is a summary of using these microorganisms as new potential biological resources, and a review of almost all of the selective isolation methods, including pretreatment and enrichment techniques that have been developed to date for the isolation of rare actinomycetes.

Characterizing the native codon usages of a genome: an axis projection approach

Codon usage can provide insights into the nature of the genes in a genome. Genes that are “native” to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias “typical” usage to a more biased “high-expression” usage characteristic of genes encoding abundant proteins. Genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. In this study, we present a method for characterizing the codon usages of native genes—both typical and highly expressed—within a genome. Each gene is evaluated relative to a half line (or axis) in a 59D space of codon usage. The axis begins at the modal codon usage, the usage that matches the largest number of genes in the genome, and it passes through a point representing the codon usage of a set of genes with expression-related bias. A gene whose codon usage matches (does not significantly differ from) a point on this axis is a candidate native gene, and the location of its projection onto the axis provides a general estimate of its expression level. A gene that differs significantly from all points on the axis is a candidate foreign gene. This automated approach offers significant improvements over existing methods. We illustrate this by analyzing the genomes of Pseudomonas aeruginosa PAO1 and Bacillus anthracis A0248, which can be difficult to analyze with commonly used methods due to their biased base compositions. Finally, we use this approach to measure the proportion of candidate foreign genes in 923 bacterial and archaeal genomes. The organisms with the most homogeneous genomes (containing the fewest candidate foreign genes) are mostly endosymbionts and parasites, though with exceptions that include Pelagibacter ubique and Beutenbergia cavernae. The organisms with the most heterogeneous genomes (containing the most candidate foreign genes) include members of the genera Bacteroides, Corynebacterium, Desulfotalea, Neisseria, Xylella, and Thermobaculum.

Koreibacter algae gen. nov., sp. nov., isolated from seaweed

A Gram-positive, aerobic, non-motile, rod-shaped actinomycete, designated strain DSW-2T, was isolated from a seaweed sample collected around Mara Island, Jeju, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that strain DSW-2T belongs to the suborder Micrococcineae and forms a distinct clade separated from representatives of the several families of this order. Levels of 16S rRNA gene sequence similarity between the novel strain and members of this suborder were lower than 96.4 %. The peptidoglycan type is A3α with Lys–Ser as the interpeptide bridge. Whole-cell sugars are glucose and galactose. The major menaquinone is MK-9(H4). The predominant fatty acid is ai-C15 : 0. The polar lipids are phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 68.3 mol%. On the basis of the chemotaxonomic markers and phylogenetic distinctiveness presented here, it is evident that the isolate represents a novel taxon within the suborder Micrococcineae. The name Koreibacter algae gen. nov., sp. nov. is proposed, with the type strain DSW-2T (=KCTC 13436T =DSM 22126T).

Miniimonas arenae gen. nov., sp. nov., an actinobacterium isolated from sea sand

A Gram-positive, non-motile, coccoid- to rod-shaped, non-spore-forming bacterium, designated strain YM18-15(T), was isolated from sea sand and studied using a polyphasic taxonomic approach. Strain YM18-15(T) grew under both aerobic and anaerobic conditions. The cell-wall peptidoglycan type was A4β and ornithine was the diagnostic diamino acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown phospholipid, MK-8(H(4)) was the major menaquinone and the predominant fatty acids were anteiso-C(15 : 0) and C(16 : 0). The DNA G+C content was 74.2 mol%. High 16S rRNA gene sequence similarities (96.3-97.3 %) were found with the sequences of the type strains of the three genera of the family Beutenbergiaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YM18-15(T) formed a clade with Serinibacter salmoneus, Salana multivorans and Beutenbergia cavernae. Strain YM18-15(T) differed from these three type strains in chemotaxonomic characteristics and in 16S rRNA gene signature nucleotides. Based on genetic and chemotaxonomic evidence, it is suggested that strain YM18-15(T) represents a novel species of a new genus within the family Beutenbergiaceae, for which the name Miniimonas arenae gen. nov., sp. nov. is proposed. The type strain of the type species is YM18-15(T) (=NBRC 106267(T)=KCTC 19750(T)=MBIC 08348(T)).

Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm

A novel actinomycete, strain OFN S31(T), was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31(T) formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31(T) (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31(T) is characterized by the absence of mycelium and mycolic acids. Strain OFN S31(T) had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31(T) is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31(T) (=CIP 109864(T) =DSM 45258(T)).

Serinibacter salmoneus gen. nov., sp. nov., an actinobacterium isolated from the intestinal tract of a fish, and emended descriptions of the families Beutenbergiaceae and Bogoriellaceae

A novel Gram-positive bacterium, designated Kis4-28(T), was isolated from the intestinal tract of a fish, and its taxonomic position was investigated by a polyphasic approach. The sample was collected from the coast of Tokyo Bay, Japan. Cells of strain Kis4-28(T) were rod-shaped, non-motile and non-sporulating. The peptidoglycan type of the isolate was A4alpha; lysine was the diagnostic diamino acid. The only menaquinone detected was MK-8(H(4)), and the major fatty acids were anteiso-C(15 : 0) and C(16 : 0). Galactose was detected as a major cell-wall sugar. The polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 70.7 mol%. 16S rRNA gene sequence analysis revealed that strain Kis4-28(T) and the type strain of Salana multivorans formed a monophyletic cluster with a 16S rRNA gene sequence similarity of 96.2 %. Strain Kis4-28(T) was clearly distinguishable from the genus Salana in terms of its chemotaxonomic characteristics. On the basis of the genotypic and phenotypic characteristics, a new genus and species is proposed for strain Kis4-28(T), with the name Serinibacter salmoneus gen. nov., sp. nov. The type strain of Serinibacter salmoneus is Kis4-28(T) (=NBRC 104924(T) =DSM 21801(T)). In addition, on the basis of 16S rRNA gene sequence analysis of the genus Serinibacter and related genera, emended descriptions of the families Beutenbergiaceae and Bogoriellaceae are proposed to accommodate the genera Beutenbergia, Salana and Serinibacter, and the genera Bogoriella and Georgenia, respectively.

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122)

Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. B. cavernae HKI 0122^T is a Gram-positive, non-motile, non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell wall peptidoglycan contains the diagnostic L-lysine ← L-glutamate interpeptide bridge. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the poorly populated micrococcineal family Beutenbergiaceae, and this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa

The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.

Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia

A Gram-positive, motile, short-rod-shaped strain, designated YIM 004T, was isolated from a forest-soil sample collected from Lijiang, Yunnan Province, China, and was investigated using a polyphasic taxonomic approach. The isolate contained chemotaxonomic markers that corresponded to those of its phylogenetic neighbour, Georgenia muralis, i.e. it possessed peptidoglycan type A4α with lysine as the diagnostic cell-wall diamino acid, the predominant menaquinone was MK-8(H4) and the major fatty acid was ai-C15 : 0. The G+C content of the genomic DNA was 72.9 mol%. Strain YIM 004T exhibited a 16S rRNA gene sequence similarity of 97.3 % and a DNA–DNA relatedness value of 18 % with respect to G. muralis DSM 14418T. On the basis of the phenotypic and genotypic differences between the isolate and G. muralis, strain YIM 004T represents a novel species of the genus Georgenia, for which the name Georgenia ruanii sp. nov. is proposed. The type strain is YIM 004T (=CCTCC AB 204065T=DSM 17458T=KCTC 19029T). In addition, an emended description of the genus Georgenia is presented.

Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae

A Gram-positive, coccoid, non-spore-forming bacterium, designated strain 3-6T, was isolated from farmland soil and subjected to a polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbour was the type strain of Georgenia muralis (94.2 % 16S rRNA gene sequence similarity). Chemotaxonomic characteristics of strain 3-6T were as follows: the major menaquinone was MK-8(H4); the polar lipids consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid; the predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; mycolic acids were absent. A new murein type, l-lys–gly–l-glu–l-Glu (A4α), was found in the peptidoglycan of the cell wall. The DNA G+C content was 69.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, it is suggested that strain 3-6T represents a novel species of a new genus within the suborder Micrococcineae, for which the name Ruania albidiflava gen. nov., sp. nov. is proposed. The type strain of Ruania albidiflava is 3-6T (=CGMCC 4.3142T=DSM 18029T=JCM 13910T=PCM 2644T).

Streptomonospora alba sp. nov., a novel halophilic actinomycete, and emended description of the genus Streptomonospora Cui et al. 2001

A halophilic actinomycete, strain YIM 90003(T), was isolated from a soil sample collected from Xinjiang Province, China, by using starch-casein agar with a salt concentration of 20 % (w/v), pH 7.0. The strain grew well on most media tested. No diffusible pigment was produced. Aerial mycelium and substrate mycelium were well developed on most media. The aerial mycelium formed short spore chains, bearing non-motile, straight to flexuous spores with wrinkled surfaces. The cell walls of strain YIM 90003(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. Cell-wall hydrolysates contained galactose and arabinose. Menaquinone composition varied with the medium used for cell cultivation; on glucose-yeast extract medium supplemented with 10 % NaCl, the major menaquinone was MK-9(H(4)), while, on vitamin-enriched ISP 2 medium, the major menaquinones were MK-10(H(2)), MK-9(H(8)) and MK-10(H(4)). Phospholipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, diphosphatidyl glycerol, methylphosphatidylethanolamine, phosphatidylserine, phosphatidylcholine and an unidentified phospholipid. 16S rRNA gene sequence analysis showed Streptomonospora salina as the closest phylogenetic neighbour. On the basis of these analyses, strain YIM 90003(T) is a member of the genus Streptomonospora, though its properties do not match the generic description fully with respect to the menaquinone composition and peptidoglycan amino acid. Analyses of mechanically disrupted cell walls of the type species, Streptomonospora salina DSM 44593(T), and strain YIM 90003(T), purified by tryptic digestion and subsequent SDS treatment, revealed the exclusive presence of meso-diaminopimelic acid as the diagnostic diamino acid of peptidoglycan. Thus, the genus description of Streptomonospora, indicating the presence of several amino acids usually not found in the peptidoglycan moiety, is therefore emended. DNA-DNA hybridization and comparison of physiological and chemotaxonomic characteristics demonstrated strain YIM 90003(T) to be different from Streptomonospora salina. The name Streptomonospora alba sp. nov. is proposed, with strain YIM 90003(T) (=CCTCC AA001013(T)=DSM 44588(T)) as the type strain.

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

SUMMARY

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Search and discovery strategies for biotechnology: the paradigm shift

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Strategies for discovering drugs from previously unexplored natural products

Natural products are the most consistently successful source of drug leads. Despite this, their use in drug discovery has fallen out of favour. Natural products continue to provide greater structural diversity than standard combinatorial chemistry and so they offer major opportunities for finding novel low molecular weight lead structures that are active against a wide range of assay targets. As less than 10% of the world's biodiversity has been tested for biological activity, many more useful natural lead compounds are awaiting discovery. The challenge is how to access this natural chemical diversity.