Growing unculturable bacteria

The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.     

Cultivation of unculturable soil bacteria

Despite the abundance of bacterial species in soil, more than 99% of these species cannot be cultured by traditional techniques. In addition, the less than 1% of bacteria that can be cultured are not representative of the total phylogenetic diversity. Hence, identifying novel species and their new functions is still an important task for all microbiologists. Cultivating techniques have played an important role in identifying new species but are still low-throughput processes. This review discusses the issues surrounding cultivation, including achievements, limitations, challenges, and future directions.     

Challenges and perspectives in vaccination against leishmaniasis

The leishmaniases are a group of diseases caused by protozoa of the genus Leishmania and affect millions of people worldwide. The leishmaniases are transmitted to vertebrate hosts by phlebotomine sand flies. In this review, we focus on several issues that have been poorly addressed in ongoing efforts to develop a vaccine against Leishmania, namely: vaccination with antigens present in sand fly saliva, vaccines based on intracellular Leishmania antigens, and use of recombinant BCG as a vehicle for vaccination. Additionally, we address the differences between L. major and L. braziliensis and the impact that these differences may have on strategies for immunoprophylaxis.     

Exopolysaccharides from lactic acid bacteria: perspectives and challenges

Some lactic acid bacteria (LAB) secrete a polysaccharide polymer. This extracellular polysaccharide, or "exopolysaccharide" (EPS), is economically important because it can impart functional effects to foods and confer beneficial health effects. LAB have a "Generally Recognized As Safe" (GRAS) classification and are likely candidates for the production of functional EPSs. Current challenges are to improve the productivity of EPSs from LAB and to produce EPSs of a structure and size that impart the desired functionality. The engineering of improvements in these properties will depend on a deep understanding of the EPS biosynthetic metabolism and of how the structure of EPSs relates to a functional effect when incorporated into a food matrix.     

Longevity of bacteria: Considerations in environmental release

Microbial growth theory has been developed primarily for laboratory culture. With increased opportunity for release of beneficial organisms, including those that have been genetically engineered, into the environment, it is important to understand microbial behavior under natural conditions in which there is usually severe nutrient limitation. By investigation of the survival of three beneficial soil bacteria in distilled water, the surprising observation was made of cell longevities in excess of a year without substrate input. It is suggested that this could result from the utilization of dead cells within the population and from the viable cells' having a very low maintenance energy requirement, thus placing the cell in a state of arrested metabolism.     

Lactic acid bacteria and proteomics: current knowledge and perspectives

Lactic acid bacteria (LAB) are widely used in the agro-food industry. Some of the LAB also participate in the natural flora in humans and animals. We review here proteomic studies concerning LAB. Two methods of research can be distinguished. In the first one, a systematic mapping of proteins is attempted, which will be useful for taxonomy and to function assignment of proteins. The second one focuses particularly on proteins whose synthesis is induced by various environmental situations or stresses. However, both approaches are complementary and will give new insights for the use of bacteria in industry, in human health and in the struggle against bacterial pathogens. Interest in LAB is growing, showing thus an increasing concern of their rational use and one can foresee in the near future an increasing use of proteomics as well as genomics.     

Challenges in applying microarrays to environmental studies

Although DNA microarray technology has been used successfully to analyze global gene expression in pure cultures, it has not been rigorously tested and evaluated within the context of complex environmental samples. Adapting microarray hybridization for use in environmental studies faces several challenges associated with specificity, sensitivity and quantitation.     

Biotechnological production of polyamines by bacteria: recent achievements and future perspectives

In Bacteria, the pathways of polyamine biosynthesis start with the amino acids l-lysine, l-ornithine, l-arginine, or l-aspartic acid. Some of these polyamines are of special interest due to their use in the production of engineering plastics (e.g., polyamides) or as curing agents in polymer applications. At present, the polyamines for industrial use are mainly synthesized on chemical routes. However, since a commercial market for polyamines as well as an industry for the fermentative production of amino acid exist, and since bacterial strains overproducing the polyamine precursors l-lysine, l-ornithine, and l-arginine are known, it was envisioned to engineer these amino acid-producing strains for polyamine production. Only recently, researchers have investigated the potential of amino acid-producing strains of Corynebacterium glutamicum and Escherichia coli for polyamine production. This mini-review illustrates the current knowledge of polyamine metabolism in Bacteria, including anabolism, catabolism, uptake, and excretion. The recent advances in engineering the industrial model bacteria C. glutamicum and E. coli for efficient production of the most promising polyamines, putrescine (1,4-diaminobutane), and cadaverine (1,5-diaminopentane), are discussed in more detail.     

Phylogenetic perspectives on nodulation: evolving views of plants and symbiotic bacteria

Phylogenetic studies are contributing greatly to our knowledge of relationships on both sides of the plant–bacteria nodulation symbiosis. Multiple origins of nodulation (perhaps even within the legume family) appear likely. However, all nodulating flowering plants are more closely related than previously suspected, suggesting that the predisposition to nodulate might have arisen only once. Phylogenies of 16S rRNA genes highlight the evolutionary diversity of symbiotic bacteria and appear to rule out any broad coevolution with their plant hosts, but high levels of gene transfer might obscure the relevant pattern. The origins of nodulation, and the extent to which developmental programs are conserved in nodules remain unclear, but an improved understanding of the relationships between nodulin genes is providing some clues.     

Thermophilic,lignocellulolytic bacteria for ethanol production: current state and perspectives

Lignocellulosic biomass contains a variety of carbohydrates, and their conversion into ethanol by fermentation requires an efficient microbial platform to achieve high yield, productivity, and final titer of ethanol. In recent years, growing attention has been devoted to the development of cellulolytic and saccharolytic thermophilic bacteria for lignocellulosic ethanol production because of their unique properties. First of all, thermophilic bacteria possess unique cellulolytic and hemicellulolytic systems and are considered as potential sources of highly active and thermostable enzymes for efficient biomass hydrolysis. Secondly, thermophilic bacteria ferment a broad range of carbohydrates into ethanol, and some of them display potential for ethanologenic fermentation at high yield. Thirdly, the establishment of the genetic tools for thermophilic bacteria has allowed metabolic engineering, in particular with emphasis on improving ethanol yield, and this facilitates their employment for ethanol production. Finally, different processes for second-generation ethanol production based on thermophilic bacteria have been proposed with the aim to achieve cost-competitive processes. However, thermophilic bacteria exhibit an inherent low tolerance to ethanol and inhibitors in the pretreated biomass, and this is at present the greatest barrier to their industrial application. Further improvement of the properties of thermophilic bacteria, together with the optimization production processes, is equally important for achieving a realistic industrial ethanol production.     

Biotechnological production of cellulose by acetic acid bacteria: current state and perspectives

Applied Microbiology and Biotechnology - Bacterial cellulose is an attractive biopolymer for a number of applications including food, biomedical, cosmetics, and engineering fields. In addition to...     

Nickel-resistance-based minitransposons: new tools for genetic manipulation of environmental bacteria

The ncc and nre nickel resistance determinants from Ralstonia eutropha-like strain 31A were used to construct mini-Tn5 transposons. Broad host expression of nickel resistance was observed for the nre minitransposons in members of the alpha, beta, and gamma subclasses of the Proteobacteria, while the ncc minitransposons expressed nickel resistance only in R. eutropha-like strains.     

Challenges and perspectives for species distribution modelling in the neotropics

The workshop 'Species distribution models: applications, challenges and perspectives' held at Belo Horizonte (Brazil), 29-30 August 2011, aimed to review the state-of-the-art in species distribution modelling (SDM) in the neotropical realm. It brought together researchers in ecology, evolution, biogeography and conservation, with different backgrounds and research interests. The application of SDM in the megadiverse neotropics-where data on species occurrences are scarce-presents several challenges, involving acknowledging the limitations imposed by data quality, including surveys as an integral part of SDM studies, and designing the analyses in accordance with the question investigated. Specific solutions were discussed, and a code of good practice in SDM studies and related field surveys was drafted.     

Engineering bacteria toward tumor targeting for cancer treatment: current state and perspectives

One of the primary limitations of cancer therapy is lack of selectivity of therapeutic agents to tumor cells. Current efforts are focused on discovering and developing anticancer agents that selectively target only tumor cells and spare normal cells to improve the therapeutic index. The use of preferentially replicating bacteria as an oncolytic agent is one of the innovative approaches for the treatment of cancer. This is based on the observation that some obligate or facultative anaerobic bacteria are capable of multiplying selectively in tumors and inhibiting their growth. Meanwhile, bacteria have been demonstrated to colonize and destroy tumor, and have emerged as biological gene vectors to tumor microenvironment. To improve the efficacy and safety of the bacterial therapy, a further understanding of bacteria between with immune system is required. Furthermore, we want to evaluate how bacterial infection facilitates the “bystander effect” of chemotherapeutic agent and assess if it can be used for additional antitumor effect when combined with chemotherapy. This study may not only evaluate therapeutic efficacy of bacteria for the treatment of cancer but also elucidate the mechanisms underlying antitumor activities mediated by bacteria, which involve host immune responses and the cellular molecular responses.