Tapping into microbial diversity

Therapeutic potential of natural product signal transduction agents

Modern drug discovery embraces a strategy of targeting cellular signal transduction pathways as a means of finding new therapeutic agents. Historically, natural products derived from microorganisms have played an important role as drug leads and clinical candidates under this paradigm. The future drug potential of natural products as signal transduction agents looks promising, as illustrated by two key examples. First, substantial advances have been made in the development of inhibitors based on immunophilin ligand polyketides, which target the TOR-mediated pathways and can modulate processes including cell proliferation and cell-cycle arrest. Second, the discovery of natural product inhibitors of the ubiquitin-proteasome proteolytic signal transduction pathway represents an emerging field. Given these examples, together with the diversity of as yet undiscovered agents, natural product signal transduction agents offer great potential for future drug discovery efforts.

A molecular microbial ecology approach to studying hemodialysis water and fluid

Bacteria, or bacteria-derived products, might be responsible for deleterious effects in hemodialysis patients. Most microorganisms in hemodialysis water, including potential pathogens, are difficult to isolate and might subsist in a 'viable but not culturable' state or may need specific culture media. A molecular culture-independent approach based on the analysis of the 16S rDNA obtained from total DNA has been used to better know the diversity of bacteria inhabiting hemodialysis water and fluid, and to address the possible health effects associated with their presence. Four clone libraries from 16S rDNA (274 clones) were analyzed to characterize the species or groups of bacteria present, to assess their distribution in the water circuit, and to compare the results with those previously obtained in culture-dependent analysis. One hundred and ninety-seven clones of four gene libraries were analyzed by sequencing, and were identified phylogenetically. Clones affiliated to the Alphaproteobacteria group led the diversity. The presence in several samples of Alpha-4-proteobacteria, recognized as sphingolipids producers, was to be noted. The most abundant clones were affiliated to the Betaproteobacteria branch, closely related to the genus Herbaspirillum. As known, Alphaproteobacteria and Betaproteobacteria genomes might present a manifest excess in CpG sequences and most of them show a lipopolysaccharide-rich outer membrane, both described as inducers of innate immunity responses. Another abundant group, belonging to the Cyanobacteria class, a possible source of cyanotoxins, was not related to any previously cultured bacterium. Possible risk implications for hemodialysis patients of the bacterial community detected are discussed.

Cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study

An evolutionary algorithm was applied to study the complex interactions between medium parameters and their effects on the isolation of denitrifying bacteria, both in number and in diversity. Growth media with a pH of 7 and a nitrogen concentration of 3 mM, supplemented with 1 ml of vitamin solution but not with sodium chloride or riboflavin, were the most successful for the isolation of denitrifiers from activated sludge. The use of ethanol or succinate as a carbon source and a molar C/N ratio of 2.5, 20, or 25 were also favorable. After testing of 60 different medium parameter combinations and comparison with each other as well as with the standard medium Trypticase soy agar supplemented with nitrate, three growth media were highly suitable for the cultivation of denitrifying bacteria. All evaluated isolation conditions were used to study the cultivable denitrifier diversity of activated sludge from a municipal wastewater treatment plant. One hundred ninety-nine denitrifiers were isolated, the majority of which belonged to the Betaproteobacteria (50.4%) and the Alphaproteobacteria (36.8%). Representatives of Gammaproteobacteria (5.6%), Epsilonproteobacteria (2%), and Firmicutes (4%) and one isolate of the Bacteroidetes were also found. This study revealed a much more diverse denitrifying community than that previously described in cultivation-dependent research on activated sludge.

Capturing the uncultivated majority

The metagenomic analysis of environmental microbial communities continues to be a rapidly developing area of study. DNA isolation, the first step in capturing the uncultivated majority, has seen many advances in recent years. Protocols have been developed to distinguish DNA from live versus dead cells and to separate extracellular from intracellular DNA. Looking to increase our understanding of the role that members of a microbial community play in ecological processes, several techniques have been developed that are enabling greater in-depth analysis of environmental metagenomes. These include the development of environmental gene tags and the serial analysis of 16S rRNA gene sequence tags. In addition, new screening methods have been designed to select for specific functional genes within metagenomic libraries. Finally, new cultivation methods continue to be developed to improve our ability to capture a greater diversity of microorganisms within the environment.

Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics

The novel candidate phylum Poribacteria is specifically associated with several marine demosponge genera. Because no representatives of Poribacteria have been cultivated, an environmental genomic approach was used to gain insights into genomic properties and possibly physiological/functional features of this elusive candidate division. In a large-insert library harbouring an estimated 1.1 Gb of microbial community DNA from Aplysina aerophoba, a Poribacteria-positive 16S rRNA gene locus was identified. Sequencing and sequence annotation of the 39 kb size insert revealed 27 open reading frames (ORFs) and two genes for stable RNAs. The fragment exhibited an overall G+C content of 50.5% and a coding density of 86.1%. The 16S rRNA gene was unlinked from a conventional rrn operon. Its flanking regions did not show any synteny to other 16S rRNA encoding loci from microorganisms with unlinked rrn operons. Two of the predicted hypothetical proteins were highly similar to homologues from Rhodopirellula baltica. Furthermore, a novel kind of molybdenum containing oxidoreductase was predicted as well as a series of eight ORFs encoding for unusual transporters, channel or pore forming proteins. This environmental genomics approach provides, for the first time, genomic and, by inference, functional information on the so far uncultivated, sponge-associated candidate division Poribacteria.

Empirical antibacterial drug discovery—Foundation in natural products

Natural products have been a rich source in providing leads for the development of drugs for the treatment of bacterial infections. However, beyond the discovery of the natural product, thienamycin and the synthetic lead, oxazolidinone in the 1970s, there has been a dearth of new compounds. This commentary provides an overview of current antibiotic leads and their mechanism of action, and highlights tools that can be applied to the discovery of new antibiotics.

Metagenomics-based drug discovery and marine microbial diversity

As the global threat of drug-resistant pathogens continues to rise, new strategies and resources are required to accelerate and advance the drug discovery process. We believe that rapid progress in metagenomics has opened up a new era in the study of marine microbial diversity that enables direct access to the genomes of numerous uncultivable microorganisms. This review outlines recent developments and future trends in metagenomics-based drug discovery in marine microbial communities and their associated chemical prosperity.

The Impact of Bacterial Genomics on Natural Product Research

"There's life in the old dog yet!" This adage also holds true for natural product research. After the era of natural products was declared to be over, because of the introduction of combinatorial synthesis techniques, natural product research has taken a surprising turn back towards a major field of pharmaceutical research. Current challenges, such as emerging multidrug-resistant bacteria, might be overcome by developments which combine genomic knowledge with applied biology and chemistry to identify, produce, and alter the structure of new lead compounds. Significant biological activity is reported much less frequently for synthetic compounds, a fact reflected in the large proportion of natural products and their derivatives in clinical use. This Review describes the impact of microbial genomics on natural products research, in particularly the search for new lead structures and their optimization. The limitations of this research are also discussed, thus allowing a look into future developments.

Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags

Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82(o)N). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.

Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study

BACKGROUND

Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. Here, we used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. Nitrilases are relatively rare in bacterial genomes, their biological function being unclear.

RESULTS

We examined the genetic neighborhood of the different subfamily genes and discovered conserved gene clusters or operons associated with specific nitrilase clades. The inferred evolutionary transitions that separate nitrilases which belong to different gene clusters correlated with changes in their enzymatic properties. We present evidence that Darwinian adaptation acted during one of those transitions and identified sites in the enzyme that may have been under positive selection.

CONCLUSION

Changes in the observed biochemical properties of the nitrilases associated with the different gene clusters are consistent with a hypothesis that those enzymes have been recruited to a novel metabolic pathway following gene duplication and neofunctionalization. These results demonstrate the benefits of combining environmental genomic sampling and completed genomes data with evolutionary and biochemical analyses in the study of gene families. They also open new directions for studying the functions of nitrilases and the genes they are associated with.

Exploring novel bioactive compounds from marine microbes

The historical paradigm of the deep ocean as a biological 'desert' has shifted to one of a 'rainforest' owing to the isolation of many novel microbes and their associated bioactive compounds. Recently, there has been an explosion of information about novel bioactive compounds that have been isolated from marine microbes in an effort to further explore the relatively untapped marine microbes and their secondary metabolites for drug discovery. The microbes are recovered and purified from the ocean by both conventional and innovative isolation methods to obtain those previously thought to be 'uncultivable'. To overcome the difficulties and limitations associated with cultivation techniques, several DNA-based molecular methods have been developed to bypass the culture-dependent bottleneck. Bioactive compounds isolated using the above strategies have not only shown importance in biotechnological and pharmaceutical applications but have also increased our understanding of the diversity of marine microbiota, ecosystem functions and the exploitable biology.

Whither or wither geomicrobiology in the era of 'community metagenomics'

Molecular techniques are valuable tools that can improve our understanding of the structure of microbial communities. They provide the ability to probe for life in all niches of the biosphere, perhaps even supplanting the need to cultivate microorganisms or to conduct ecophysiological investigations. However, an overemphasis and strict dependence on such large information-driven endeavours as environmental metagenomics could overwhelm the field, to the detriment of microbial ecology. We now call for more balanced, hypothesis-driven research efforts that couple metagenomics with classic approaches.

Marine actinomycete diversity and natural product discovery

Microbial natural products remain an important resource for drug discovery yet the microorganisms inhabiting the world's oceans have largely been overlooked in this regard. The recent discovery of novel secondary metabolites from taxonomically unique populations of marine actinomycetes suggests that these bacteria add an important new dimension to microbial natural product research. Continued efforts to characterize marine actinomycete diversity and how adaptations to the marine environment affect secondary metabolite production will create a better understanding of the potential utility of these bacteria as a source of useful products for biotechnology.

New method to characterize microbial diversity using flow cytometry

The majority of microorganisms have yet to be cultivated and represent a vast uncharacterized and untapped resource. Here, we report the utilization of a combination of flow cytometry, cultivation, and molecular genetics to develop new methodologies to access and characterize biodiversity in microbial samples. We demonstrate that fluorescent dyes and combinations of dyes can selectively stain portions of bacterial populations that can be isolated as sub-populations using fluorescence-activated cell sorting (FACS). Microbial sub-populations obtained by FACS differ substantially from the original microbial population, as demonstrated by denaturing gradient gel electrophoresis and determination of 16S rRNA gene sequences. These sub-populations can subsequently be used to inoculate microbial growth media, allowing the isolation of different microbial species from those that can be readily cultivated from the original sample using the same microbial growth media. When this technique was applied to the analysis of activated-sludge and Yellowstone Lake hydrothermal vent samples, comparative analysis of 16S rDNA sequences revealed that FACS allowed the detection of numerous bacterial species, including previously unknown species, not readily detectable in the original sample due to low relative abundance. This approach may result in a convenient methodology to more thoroughly characterize microbial biodiversity.

Cold adaptation in the Antarctic Archaeon Methanococcoides burtonii involves membrane lipid unsaturation

Direct analysis of membrane lipids by liquid chromatography-electrospray mass spectrometry was used to demonstrate the role of unsaturation in ether lipids in the adaptation of Methanococcoides burtonii to low temperature. A proteomics approach using two-dimensional liquid chromatography-mass spectrometry was used to identify enzymes involved in lipid biosynthesis, and a pathway for lipid biosynthesis was reconstructed from the M. burtonii draft genome sequence. The major phospholipids were archaeol phosphatidylglycerol, archaeol phosphatidylinositol, hydroxyarchaeol phosphatidylglycerol, and hydroxyarchaeol phosphatidylinositol. All phospholipid classes contained a series of unsaturated analogues, with the degree of unsaturation dependent on phospholipid class. The proportion of unsaturated lipids from cells grown at 4 degrees C was significantly higher than for cells grown at 23 degrees C. 3-Hydroxy-3-methylglutaryl coenzyme A synthase, farnesyl diphosphate synthase, and geranylgeranyl diphosphate synthase were identified in the expressed proteome, and most genes involved in the mevalonate pathway and processes leading to the formation of phosphatidylinositol and phosphatidylglycerol were identified in the genome sequence. In addition, M. burtonii encodes CDP-inositol and CDP-glycerol transferases and a number of homologs of the plant geranylgeranyl reductase. It therefore appears that the unsaturation of lipids may be due to incomplete reduction of an archaeol precursor rather than to a desaturase mechanism. This study shows that cold adaptation in M. burtonii involves specific changes in membrane lipid unsaturation. It also demonstrates that global methods of analysis for lipids and proteomics linked to a draft genome sequence can be effectively combined to infer specific mechanisms of key biological processes.

High-throughput cultivation of microorganisms using microcapsules

This chapter describes a universal and novel method that provides access to the immense reservoir of untapped microbial diversity by cultivation. This technique uses microcapsules to encapsulate single cells combined with parallel microbial cultivation under low nutrient flux conditions. Under these conditions, single encapsulated cells grow and form microcolonies within the microcapsules. Flow cytometry is used as a sensitive tool to detect growth within the microcapsules. Microcapsules that contain microcolonies (originated from a single encapsulated cell) are sorted individually into microtiter dishes containing organic-rich medium. This high-throughput cultivation can provide more than 10,000 bacterial and fungal isolates per environmental sample.