Identification of indole derivatives as self-growth inhibitors of Symbiobacterium thermophilum, a unique bacterium whose growth depends on coculture with a Bacillus sp

Interspecific cross-talk: The catalyst driving microbial biosynthesis of secondary metabolites

Microorganisms co-exist and co-evolve in nature, forming intricate ecological communities. The interspecies cross-talk within these communities creates and sustains their great biosynthetic potential, making them an important source of natural medicines and high-value-added chemicals. However, conventional investigations into microbial metabolites are typically carried out in pure cultures, resulting in the absence of specific activating factors and consequently causing a substantial number of biosynthetic gene clusters to remain silent. This, in turn, hampers the in-depth exploration of microbial biosynthetic potential and frequently presents researchers with the challenge of rediscovering compounds. In response to this challenge, the coculture strategy has emerged to explore microbial biosynthetic capabilities and has shed light on the study of cross-talk mechanisms. These elucidated mechanisms will contribute to a better understanding of complex biosynthetic regulations and offer valuable insights to guide the mining of secondary metabolites. This review summarizes the research advances in microbial cross-talk mechanisms, with a particular focus on the mechanisms that activate the biosynthesis of secondary metabolites. Additionally, the instructive value of these mechanisms for developing strategies to activate biosynthetic pathways is discussed. Moreover, challenges and recommendations for conducting in-depth studies on the cross-talk mechanisms are presented.

Enhancing chemical and biological diversity by co-cultivation

In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.

Horizontal gene transfer drives the evolution of dependencies in bacteria

Many naturally occurring bacteria lead a lifestyle of metabolic dependency for crucial resources. We do not understand what factors drive bacteria toward this lifestyle and how. Here, we systematically show the crucial role of horizontal gene transfer (HGT) in dependency evolution in bacteria. Across 835 bacterial species, we map gene gain-loss dynamics on a deep evolutionary tree and assess the impact of HGT and gene loss on metabolic networks. Our analyses suggest that HGT-enabled gene gains can affect which genes are later lost. HGT typically adds new catabolic routes to bacterial metabolic networks, leading to new metabolic interactions between bacteria. We also find that gaining new routes can promote the loss of ancestral routes (”coupled gains and losses”, CGLs). Phylogenetic patterns indicate that both dependencies—mediated by CGLs and those purely by gene loss—are equally likely. Our results highlight HGT as an important driver of metabolic dependency evolution in bacteria.

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Metabolic dependencies are widespread across bacterial genomes

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New genes expand bacterial catabolism via the process of horizontal gene transfer

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During evolution, efficient pathways are gained, whereas redundant pathways are lost

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Gained pathways often depend on the metabolic byproducts of the surrounding community

Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance

Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.

Rototrichous: a new type of bacterial flagellation

A rod-shaped microorganism with unknown type of flagellation has been accidentally discovered during phase-contrast microscopy of a sample of contaminated human donor blood. The flagellum consists of three fragments that form a complex locomotor device attached to bacterial body. The device provides bacterial motility by rotating around longitudinal axis of bacterial body and so this type of flagellation has been named "rototrichous." This newly discovered bacterial flagellation should be included in the classification of bacterial flagellations.

Indole trimers with antibacterial activity against Gram-positive organisms produced using combinatorial biocatalysis

The I100V isoform of toluene-4-monooxygenase was used to catalyze the oxidative polymerization of anthranil and various indoles under mildly acidic conditions, favoring the production of trimers. Compounds produced in sufficient yield were purified and tested for their ability to inhibit the growth of B. anthracis, E. faecalis, L. monocytogenes, S. aureus, and in some cases, F. tularensis. 15 of the compounds displayed promising antibacterial activity (MIC < 5 µg/ml) against one or more of the strains tested, with the best MIC values being <0.8 µg/ml. All of these compounds had good selectivity, showing minimal cytotoxicity towards HepG2 cells. The structure was solved for six of the compounds that could be crystallized, revealing that minimally two classes of indole based trimers were produced. One compound class produced was a group of substituted derivatives of the natural product 2,2-bis(3-indolyl) indoxyl. The other group of compounds identified was classified as tryptanthrin-like compounds, all having multi-ring pendant groups attached at position 11 of tryptanthrin. One compound of particular interest, SAB-J85, had a structure that suggests that any compound, with a ring structure that can be activated by an oxygenase, might serve as a substrate for combinatorial biocatalysis.

Application of a single-colony coculture technique to the isolation of hitherto unculturable gut bacteria

Molecular studies have led to postulation of a relationship between gut microbiota and certain diseases. However, because studies of hitherto uncultured species in vivo are essential for characterizing the biology and pathogenic properties of gut bacteria, techniques for culturing and isolating such bacteria must be developed. Here, a technique is described that partially overcomes the obstacles that prevent detection of interbacterial communication in vitro and are thus responsible for the failure to culture certain bacterial species. For this purpose, a ring with a membrane filter at the bottom was designed and a relatively simple nutrient medium was used instead of conventional media. Gut bacteria were cocultivated in soft agar separated by the membrane filter to simulate interbacterial communication in vitro. Use of this soft agar coculture technique led to the successful isolation of hitherto uncultured bacteria and the demonstration of multistage interbacterial communication among gut bacteria in vitro. Cultivation and isolation of single colonies of bacteria that require other bacteria for growth will enhance efforts to better understand the physiological and pathogenic roles of gut microbiota.

Interactions in the Competitive Coexistence Process of Streptomyces sp. and Escherichia coli

Competitive coexistence of different microorganism species is a fundamental ecological process in the evolution and maintenance of biodiversity. This work studied the interactions happened in the competitive coexistence process of actinomycete Streptomyces sp. and Escherichia coli from morphological and secondary metabolites perspective. We found three important interactions occurred in their successful coexistence process: medium pH was elevated, indole alkaloids with dual inhibiting effects were produced, and culture environment was spatially structured. For the weed-like superior competitor E. coli, its massive growth was suppressed by the elevated pH and the newly produced novel bisindole alkaloid hepchrome. For the inferior Streptomyces sp., its mycelium floated to the medium surface for further colonization, and the growth in liquid medium was inhibited by its self-produced alkaloids such as halichrome A, 1,1,1-Tris (3-indolyl) methane, vibrindole A, and hepchrome. The coexistence of E. coli and Streptomyces sp. was thereby achieved through reduction of spatial and energy resource overlapping and suppression of competition.

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.

The effect of a cell-to-cell communication molecule, Pseudomonas quinolone signal (PQS), produced by P. aeruginosa on other bacterial species

One of the most important factors in the development of a bacterial community is whether the bacteria are able to grow in that habitat. The regulation of bacterial growth is generally studied in relation to physicochemical conditions, however, how bacterial communities regulate themselves remains unclear. In our previous study, it was demonstrated that a cell-to-cell communication molecule, 2-heptyl-3-hydroxy-4-quinolone, referred to as the Pseudomonas quinolone signal (PQS), affects respiring-activity in Pseudomonas aeruginosa without requiring its cognate receptor PqsR. The results suggested that PQS may affect other bacterial species, which was further examined in this study. PQS repressed the growth of several species including both Gram-negative and Gram-positive bacteria. In most cases, this effect differed from the bacteriostatic or bacteriolytic actions of antibiotics. The growth repression by PQS was inhibited when iron was added to the medium, indicating iron-chelating activity to be involved. In addition, PQS affected oxygen consumption in some species tested, and may have other underlying effects. Thus, this cell-to-cell communication molecule may influence the development of bacterial communities by regulating bacterial growth, and physicochemical factors such as iron would be important in determining its effect.

Metabolome profiling reveals metabolic cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during induced swarm motility

The metabolic cooperation in the ecosystem of Bacillus megaterium and Ketogulonicigenium vulgare was investigated by cultivating them spatially on a soft agar plate. We found that B. megaterium swarmed in a direction along the trace of K. vulgare on the agar plate. Metabolomics based on gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) was employed to analyze the interaction mechanism between the two microorganisms. We found that the microorganisms interact by exchanging a number of metabolites. Both intracellular metabolism and cell-cell communication via metabolic cooperation were essential in determining the population dynamics of the ecosystem. The contents of amino acids and other nutritional compounds in K. vulgare were rather low in comparison to those in B. megaterium, but the levels of these compounds in the medium surrounding K. vulgare were fairly high, even higher than in fresh medium. Erythrose, erythritol, guanine, and inositol accumulated around B. megaterium were consumed by K. vulgare upon its migration. The oxidization products of K. vulgare, including 2-keto-gulonic acids (2KGA), were sharply increased. Upon coculturing of B. megaterium and K. vulgare, 2,6-dipicolinic acid (the biomarker of sporulation of B. megaterium), was remarkably increased compared with those in the monocultures. Therefore, the interactions between B. megaterium and K. vulgare were a synergistic combination of mutualism and antagonism. This paper is the first to systematically identify a symbiotic interaction mechanism via metabolites in the ecosystem established by two isolated colonies of B. megaterium and K. vulgare.

Hollow-fiber membrane chamber as a device for in situ environmental cultivation

A hollow-fiber membrane chamber (HFMC) was developed as an in situ cultivation device for environmental microorganisms. The HFMC system consists of 48 to 96 pieces of porous hollow-fiber membrane connected with injectors. The system allows rapid exchange of chemical compounds, thereby simulating a natural environment. Comparative analysis through the cultivation of three types of environmental samples was performed using this newly designed device and a conventional agar-based petri dish. The results show that the ratios of novel phylotypes in isolates, species-level diversities, and cultivabilities in HFMC-based cultivation are higher than those in an agar-based petri dish for all three samples, suggesting that the new in situ cultivation device is effective for cultivation of various environmental microorganisms.

Metabolites from symbiotic bacteria

This review describes secondary metabolites that have been shown to be synthesized by symbiotic bacteria, or for which this possibility has been discussed. It includes 365 references.

Distribution of Symbiobacterium thermophilum and related bacteria in the marine environment

We study the ecological distribution of a unique syntrophic bacterium, Symbiobacterium thermophilum, and related bacteria. In this study, we found that they were frequently obtained from seashells and several marine samples. Symbiobacterium also grew from sterilized oyster shells incubated undersea for 2 or 3 months on the coast of Shimoda, Shizuoka, Japan. 16S rRNA gene-based phylogeny of the clones obtained from the Symbiobacterium-positive cultures demonstrated the potential diversity of this bacterial group, which constitutes a distinct clade between Actinobacteria and Firmicutes. We successfully isolated two new Symbiobacterium strains from oyster shells. 16S rRNA gene-based phylogeny indicated that one belongs to S. thermophilum, and that the other is affiliated with a different species. We also isolated Ureibacillius spp., which showed activity supporting the growth of S. thermophilum.