Search

• The synchronous production of CH 4 and RDOM could be widespread in inland waters. • Keystone taxa regulate the intensity of microbial cooperation. • Microbial cooperation links the synchronous production of CH 4 and RDOM. The production of both methane (CH 4) and refractory dissolved organic matter (RDOM) depends on microbial consortia in inland waters, and it is unclear yet the link of these two processes and the underlying microbial regulation mechanisms. Therefore, a large-scale survey was conducted in China's inland waters, with the measurement of CH 4 concentrations, DOM chemical composition, microbial community composition, and relative environmental parameters mainly by chromatographic, optical, mass spectrometric, and high-throughput sequencing analyses, to clarify the abovementioned questions. Here, we found a synchronous production of CH 4 and RDOM linked by microbial consortia in inland waters. The increasing microbial cooperation driven by the keystone taxa (mainly Fluviicola and Polynucleobacter) could promote the transformation of labile DOM into RDOM and meanwhile benefit methanogenic microbial communities to produce CH 4. As such, CH 4 and RDOM showed consistent spatial differences, which were mainly influenced by total nitrogen and dissolved oxygen concentrations. This finding deepened the understanding of microbial-driven carbon transformation and will help to more accurately evaluate the carbon source-sink relationship in inland waters. [Display omitted] [ABSTRACT FROM AUTHOR]

To engineer efficient microbial management strategies in the food industry, a comprehensive understanding of microbial interactions is crucial. Microorganisms live in communities where they influence each other in several ways. Although much attention has been paid to the production of antagonistic metabolites in lactic acid bacteria (LAB), research that accounts for the complexity of their ecological interactions and their dynamics remains limited. This study explores binary interactions within a mock community of 94 strains, including 23 LAB from culture collections and 71 isolated from dairy products. Using a colony-picking robot and image analysis, bidirectional interactions were measured at high throughput on solid media, where one test strain was challenged against other mock community members as the target strains. Assays of 15 test strains (14 LAB and one yeast) yielded 1,142 bidirectionally mapped interactions, classified by ecological type over seven days. The results showed variation in the strength, directionality, and type of interactions depending on the origin of the target strains. Cooperation rates increased for strains isolated from raw milk to pasteurized milk and cheese, while exploitation was more common in raw milk strains. Cooperating strains also exhibited more similar ecological behaviors than competing strains, suggesting the presence of microbial cliques. Interestingly, Lactococcus cremoris ATCC 19257 developed pink-red pigmentation when co-cultured with Pseudomonas aeruginosa. Overall, these findings present an unprecedented exploratory data set that significantly improves our understanding of microbial interactions at the system level, with potential applications in strain selection for food processes such as fermentation, bioprotection, and probiotics. • High throughput approach was developed to quantify microbial interactions. • 1142 binary interactions were measured over 7 days between LAB and dairy contaminants. • Positive and negative interactions show different dynamics. • Cooperating strains display more similar ecological behaviors than competing strains. • Ecological interaction rates differ between dairy product isolation source. [ABSTRACT FROM AUTHOR]

• Climate and nutrient loading synergistically boost R. raciborskii's competitiveness. • Antagonistic effects of climate and nutrients promote R. raciborskii blooms. • Cyanobacteria-driven altruism dominates in behavioral ecology models. • Microbes adapt to the environment by regulating metabolism and gene expression. Climate change and the trophic status of water bodies are important factors in global occurrence of cyanobacterial blooms. The aim of this study was to explore the cyanobacteria‒bacterial interactions that occur during Raphidiopsis raciborskii (R. raciborskii) blooms by conducting microcosm simulation experiments at different temperatures (20 °C and 30 °C) and with different phosphorus concentrations (0.01 mg/L and 1 mg/L) using an ecological model of microbial behavior and by analyzing microbial self-regulatory strategies using weighted gene coexpression network analysis (WGCNA). Three-way ANOVA revealed significant effects of temperature and phosphorus on the growth of R. raciborskii (P < 0.001). The results of a metagenomics-based analysis of bacterioplankton revealed that the synergistic effects of both climate and trophic changes increased the ability of R. raciborskii to compete with other cyanobacteria for dominance in the cyanobacterial community. The antagonistic effects of climate and nutrient changes favored the occurrence of R. raciborskii blooms, especially in eutrophic waters at approximately 20 °C. The species diversity and richness indices differed between the eutrophication treatment group at 20 °C and the other treatment groups. The symbiotic bacterioplankton network revealed the complexity and stability of the symbiotic bacterioplankton network during blooms and identified the roles of key species in the network. The study also revealed a complex pattern of interactions between cyanobacteria and non-cyanobacteria dominated by altruism, as well as the effects of different behavioral patterns on R. raciborskii bloom occurrence. Furthermore, this study revealed self-regulatory strategies that are used by microbes in response to the dual pressures of temperature and nutrient loading. These results provide important insights into the adaptation of microbial communities in freshwater ecosystems to environmental change and provide useful theoretical support for aquatic environmental management and ecological restoration efforts. [Display omitted] [ABSTRACT FROM AUTHOR]

[Display omitted] • Bacteria upregulated growth and energy metabolism-related genes in microalgae. • Co-culture increased NH 4 +-N removal rate by 96 % under a high C/N ratio. • Co-culture upregulated urea utilization and NH 4 +-N assimilation of microalgae. • Downregulation of fatty acid degradation led to lipid accumulation in co-culture. Microalgal-bacterial consortia can treat biogas slurry and produce high-value products. This study found that co-cultures of Desmodesmus sp. and Bacillus megaterium improved nutrient removal, biomass production, and lipid accumulation in Desmodesmus sp. Dual transcriptomic analyses revealed that B. megaterium upregulated genes associated with glycolysis, the Calvin cycle, tricarboxylic acid cycle, indole acetic acid synthesis, and fatty acid biosynthesis in Desmodesmus sp. Under a high C/N ratio, key genes involved in fatty acid degradation were downregulated, promoting lipid accumulation in co-cultured Desmodesmus sp. Effective NH 4 +-N removal in the co-culture under a high C/N ratio was attributed to microbial interactions. Desmodesmus sp. downregulated the URE gene in bacteria, inhibiting urea hydrolysis, while B. megaterium upregulated the URE and gdhA genes in microalgae, promoting urea utilization and NH 4 +-N assimilation. This study provides new insights into the transcriptional regulation in nutrient assimilation and lipid metabolism in microalgal-bacterial consortia. [ABSTRACT FROM AUTHOR]

Traditional cheesemaking processes often involve backslopping practice. However, over successive inoculations, acidification deficiencies may arise. In such cases, adding a starter is recommended to restore the ecosystem stability. This study examines the impact of an autochthonous starter composed of three Lactococcus lactis strains on a raw goat milk microbial community during their evolution. Bacterial composition and technological features (acidification and aroma) were analyzed during communities' evolution over 800 generations. 16S rRNA gene metabarcoding showed that Lactococcus lactis strains predominated. The raw goat milk community acidification capacities varied early in the evolution and then remained stable. Adding the L. lactis starter to this community stabilized the ecosystem from the beginning of the evolution. The acetoin production was associated with the starter presence, consistent with the establishment of the diacetylatis biovar strain from the starter in the raw goat milk community throughout the evolution. Increased or decreased production of some volatile organic compounds when the starter was added revealed a specific aroma footprint due to interactions between the two communities. This study showed that adding a starter could help to achieve the maximum acidification rate from the early inoculation cycles and could significantly modify the aroma profile during long-term backslopping. • A raw goat milk community and a starter coevolved during long-term backslopping. • Acidification capacities varied and then stabilized from day nineteen. • Bacterial composition stabilized during the first month. • The d iacetylactis strain from the starter settled in the co-evolving association. • A specific aromatic footprint highlighted a crosstalk between the two communities. [ABSTRACT FROM AUTHOR]

BackgroundCandida krusei has been known to exhibit communal interactions such as pellicle formation and crawling out of nutritional broth. We noticed another possible interaction on agar surfaces, where C. krusei yeast cells formed mycelia along agar surfaces toward each other. We report here the results of experiments to study this interaction.ResultsWhen C.krusei yeast cells are plated in parallel streaks, they form mycelia along agar surfaces toward other yeasts. They also detect the presence of Candida albicans and Candida glabrata across agar surfaces, while the latter two react neither to their own kind, nor to C. krusei. Secreted molecule(s) are likely involved as C.krusei does not react to heat killed C. krusei. Timing and rate of mycelia formation across distances suggests that mycelia start forming when a secreted molecule(s) on agar surface reaches a certain concentration. We detected farnesol, tyrosol and tryptophol molecules that may be involved with mycelial formation, on the agar surfaces between yeast streaks. Unexpectedly the amounts detected between streaks were significantly higher than would have expected from additive amounts of two streaks. All three Candida species secreted these molecules. When tested on agar surface however, none of these molecules individually or combined induced mycelia formation by C. krusei.ConclusionsOur data confirms another communal interaction by C. krusei, manifested by formation of mycelia by yeast cells toward their own kind and other yeasts on agar surfaces. We detected secretion of farnesol, tyrosol and tryptophol by C. krusei but none of these molecules induced this activity on agar surface making it unlikely that they are the ones utilized by this yeast for this activity.

Commensal organisms appear to play significant roles in normal homeostasis as well as in the pathogenesis of HIV infection in a number of different organ systems. On November 17th and 18th, 2016, leading researchers from around the world met to discuss their insights on advances in our understanding of HIV and the microbiome at the National Institutes of Health (NIH) in Bethesda. Dr. Elhanan Borenstein of the University of Washington gave a keynote address where he discussed new developments in systems biology which hold the promise of illuminating the pathways by which these organisms interact with human physiology. He suggested that we need to get past correlations in microbiome research by using models and informatics which incorporate metagenomics to predict functional changes in the microbiome.

Adhesin-mediated bacterial interspecies interactions are important elements in oral biofilm formation. They often occur on a species-specific level, which could determine health or disease association of a biofilm community. Among the key players involved in these processes are the ubiquitous fusobacteria that have been recognized for their ability to interact with numerous different binding partners. Fusobacterial interactions with Streptococcus mutans, an important oral cariogenic pathogen, have previously been described but most studies focused on binding to non-mutans streptococci and specific cognate adhesin pairs remain to be identified. Here, we demonstrated differential binding of oral fusobacteria to S. mutans. Screening of existing mutant derivatives indicated SpaP as the major S. mutans adhesin specific for binding to Fusobacterium nucleatum ssp. polymorphum but none of the other oral fusobacteria tested. We inactivated RadD, a known adhesin of F. nucleatum ssp. nucleatum for interaction with a number of gram-positive species, in F. nucleatum ssp. polymorphum and used a Lactococcus lactis heterologous SpaP expression system to demonstrate SpaP interaction with RadD of F. nucleatum ssp. polymorphum. This is a novel function for SpaP, which has mainly been characterized as an adhesin for binding to host proteins including salivary glycoproteins. In conclusion, we describe an additional role for SpaP as adhesin in interspecies adherence with RadD-SpaP as the interacting adhesin pair for binding between S. mutans and F. nucleatum ssp. polymorphum. Furthermore, S. mutans attachment to oral fusobacteria appears to involve species- and subspecies-dependent adhesin interactions.

The discovery that the actinobacterium Micromonospora inhabits nitrogen-fixing nodules raised questions as to its potential ecological role. The capacity of two Micromonospora strains to infect legumes other than their original host, Lupinus angustifolius, was investigated using Medicago and Trifolium as test plants. Compatible rhizobial strains were used for coinoculation of the plants because Micromonospora itself does not induce nodulation. Over 50% of nodules from each legume housed Micromonospora, and using 16S rRNA gene sequence identification, we verified that the reisolated strains corresponded to the microorganisms inoculated. Entry of the bacteria and colonization of the plant hosts were monitored using a GFP-tagged Lupac 08 mutant together with rhizobia, and by using immunogold labeling. Strain Lupac 08 was localized in plant tissues, confirming its capacity to enter and colonize all hosts. Based on studying three different plants, our results support a non-specific relationship between Micromonospora and legumes. Micromonospora Lupac 08, originally isolated from Lupinus re-enters root tissue, but only when coinoculated with the corresponding rhizobia. The ability of Micromonospora to infect and colonize different legume species and function as a potential plant-growth promoting bacterium is relevant because this microbe enhances the symbiosis without interfering with the host and its nodulating and nitrogen-fixing microbes.

It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.

Host diet is a major determinant of the composition and function of the intestinal microbiome. Less understood is the importance of diet on ingested strains with probiotic significance. We investigated the population dynamics of exogenous Lactobacillus plantarum and its interactions with intestinal bacteria in mice undergoing switches between high-fat, high-sugar (HFHSD) and low-fat, plant-polysaccharide rich (LFPPD) diets. The survival and persistence of ingested L. plantarum WCFS1 was significantly improved during mouse consumption of HFHSD and was negatively associated with the numbers of indigenous Lactobacillus species. Diet also rapidly changed the composition of the indigenous microbiota, but with some taxa differentially affected between HFHSD periods. L. plantarum was not integrated into indigenous bacterial community networks according to co-occurrence patterns but still conferred distinct effects on bacterial species diversity and microbiota stability largely in a diet-dependent manner. Metagenome predictions supported the premise that L. plantarum dampens the effects of diet on the microbiome. This strain also consistently altered the predicted genetic content in the distal gut by enriching for genes encoding glyosyltransferases and bile salt hydrolases. Our findings demonstrate the interactions between ingested, transient probiotic bacteria and intestinal bacterial communities and how they can differ depending on host diet.

Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition-specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population.

To successfully colonize the oral cavity, bacteria must directly or indirectly adhere to available oral surfaces. Fusobacterium nucleatum plays an important role in oral biofilm community development due to its broad adherence abilities, serving as a bridge between members of the oral biofilm that cannot directly bind to each other. In our efforts to characterize the molecular mechanisms utilized by F. nucleatum to physically bind to key members of the oral community, we investigated the involvement of F. nucleatum outer membrane proteins in its ability to bind to the pioneer biofilm colonizer, Streptococcus gordonii. Here, we present evidence that in addition to the previously characterized fusobacterial adhesin RadD, the interaction between F. nucleatum ATCC 23726 and S. gordonii V288 involves a second outer membrane protein, which we named coaggregation mediating protein A (CmpA). We also characterized the role of CmpA in dual-species biofilm formation with S. gordonii V288, evaluated growth-phase-dependent as well as biofilm expression profiles of radD and cmpA, and confirmed an important role for CmpA, especially under biofilm growth conditions. Our findings underscore the complex set of specific interactions involved in physical binding and thus community integration of interacting bacterial species. This complex set of interactions could have critical implications for the formation and maturation of the oral biofilms in vivo, and could provide clues to the mechanism behind the distribution of organisms inside the human oral cavity.

Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about the functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and heterotrophic bacteria from a laboratory-scale anammox bioreactor. We combine metabolic network reconstruction with metatranscriptomics to examine the gene expression of anammox and heterotrophic bacteria and to identify their potential interactions. We find that Chlorobi-affiliated bacteria may be highly active protein degraders, catabolizing extracellular peptides while recycling nitrate to nitrite. Other heterotrophs may also contribute to scavenging of detritus and peptides produced by anammox bacteria, and potentially use alternative electron donors, such as H2, acetate and formate. Our findings improve the understanding of metabolic activities and interactions between anammox and heterotrophic bacteria and offer the first transcriptional insights on ecosystem function in anammox granules.

Bacteria within communities can interact to organize their behavior. It has been unclear whether such interactions can extend beyond a single community to coordinate the behavior of distant populations. We discovered that two Bacillus subtilis biofilm communities undergoing metabolic oscillations can become coupled through electrical signaling and synchronize their growth dynamics. Coupling increases competition by also synchronizing demand for limited nutrients. As predicted by mathematical modeling, we confirm that biofilms resolve this conflict by switching from in-phase to antiphase oscillations. This results in time-sharing behavior, where each community takes turns consuming nutrients. Time-sharing enables biofilms to counterintuitively increase growth under reduced nutrient supply. Distant biofilms can thus coordinate their behavior to resolve nutrient competition through time-sharing, a strategy used in engineered systems to allocate limited resources.

Manganese (Mn) is an important metal in geochemical cycles. Some microorganisms can oxidize Mn(II) to Mn oxides, which can, in turn, affect the global cycles of other elements by strong sorption and oxidation effects. Microbe-microbe interactions have important roles in a number of biological processes. However, how microbial interactions affect Mn(II) oxidation still remains unknown. Here, we investigated the interactions between two bacteria (Arthrobacter sp. and Sphingopyxis sp.) in a co-culture, which exhibited Mn(II)-oxidizing activity, although neither were able to oxidize Mn(II) in isolation. We demonstrated that the Mn(II)-oxidizing activity in co-culture was most likely induced via contact-dependent interactions. The expressed Mn(II)-oxidizing protein in the co-culture was purified and identified as a bilirubin oxidase belonging to strain Arthrobacter. Full sequencing of the bilirubin oxidase-encoding gene (boxA) was performed. The Mn(II)-oxidizing protein and the transcripts of boxA were detected in the co-culture, but not in either of the isolated cultures. This indicate that boxA was silent in Arthrobacter monoculture, and was activated in response to presence of Sphingopyxis in the co-culture. Further, transcriptomic analysis by RNA-Seq, extracellular superoxide detection and cell density quantification by flow cytometry indicate induction of boxA gene expression in Arthrobacter was co-incident with a stress response triggered by co-cultivation with Sphingopyxis. Our findings suggest the potential roles of microbial physiological responses to stress induced by other microbes in Mn(II) oxidation and extracellular superoxide production.

Fusarium verticillioides is a mycotoxigenic fungus that is a threat to food and feed safety due to its common infection of maize, a global staple crop. A proposed strategy to combat this threat is the use of biological control bacteria that can inhibit the fungus and reduce mycotoxin contamination. In this study, the effect of multiple environmental isolates of Streptomyces on F. verticillioides was examined via transcriptome analysis. The Streptomyces strains ranged from inducing no visible response to dramatic growth inhibition. Transcriptionally, F. verticillioides responded proportionally to strain inhibition with either little to no transcript changes to thousands of genes being differentially expressed. Expression changes in multiple F. verticillioides putative secondary metabolite gene clusters was observed. Interestingly, genes involved in the fusaric acid gene cluster were suppressed by inhibitory strains of Streptomyces. A F. verticillioides beta-lactamase encoding gene (FVEG_13172) was found to be highly induced by specific inhibitory Streptomyces strains and its deletion increased visible response to those strains. This study demonstrates that F. verticillioides does not have an all or nothing response to bacteria it encounters but rather a measured response that is strain specific and proportional to the strength of inhibition.

The study aimed to identify interspecies interactions within a native microbial community present in a hydrogen-producing bioreactor fed with two wheat straw cultivars. The relationships between the microbial community members were studied building a canonical correspondence analysis and corroborated through in vitro assays. The results showed that the bioreactor reached a stable hydrogen production of ca. 86 mL/kg·d in which the cultivar change did not affect the average performance. Lactobacillus and Clostridium dominated throughout the whole operation period where butyric acid was the main metabolite. A canonical correspondence analysis correlated positively Lactobacillus with hydrogen productivity and hydrogen-producing bacteria like Clostridium and Ruminococaceae. Agar diffusion testing of isolated strains confirmed that Lactobacillus inhibited the growth of Enterococcus, but not of Clostridium. We suggest that the positive interaction between Lactobacillus and Clostridium is generated by a division of labor for degrading the lignocellulosic substrate in which Lactobacillus produces lactic acid from the sugar fermentation while Clostridium quickly uses this lactic acid to produce hydrogen and butyric acid. The significance of this work lies in the fact that different methodological approaches confirm a positive association in the duo Lactobacillus–Clostridium in a bioreactor with stable hydrogen production from a complex substrate. HIGHLIGHTS Native microbiota of wheat straw reached a stable hydrogen production.; Microbial structure was stable dominated by Lactobacillus and Clostridium.; Statistical analysis and in vitro assays demonstrated positive interactions.; Division of labor in lignocellulose consumption could promote positive interactions.;

Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance. [Display omitted] • Metabolic interactions determine the transfer of an antibiotic resistance-encoding plasmid • Negative interactions reduce population intermixing and slow plasmid transfer • Positive interactions increase population intermixing and accelerate plasmid transfer • Metabolic interactions determine the ability of plasmids to proliferate after transfer Ma et al. show that metabolic interactions determine the extent of spatial intermixing and the spatial positionings of different microbial populations during surface-associated growth. This determines the extent to which an antibiotic resistance-encoding plasmid can transfer within the system and the ability of transconjugants to proliferate after receiving the plasmid. [ABSTRACT FROM AUTHOR]

• QS language "interpreter" is proposed and reconstructed in five E. coli strains. • Linear and circular QSCN are studied experimentally and theoretically. • Micro- and macroscopic measurements are conducted for dynamics of consortia. • Model-based optimization is conducted for one-way QS signal transmission. • Stability is evaluated on signal transmission and external environment adaptation. Microbes in diverse natural communities communicate via quorum sensing (QS) signals that act as microbial languages. QS-based communications have been reconstructed in two-strain microbiota for promising consortium-based applications. However, investigation and synthesis of multiple QS signals transmission in the QS communication network (QSCN) are less explored. In this study, QS language "interpreter" was proposed and constructed in five Escherichia coli strains to simulate the linear and circular QSCN among natural microbial communities. Specifically, by combining strain-level microscopic and bulk-level macroscopic measurements, we investigate the performances and dynamics of synthetic three-strain QS language "interpreter" ecosystems that are in response to dramatic environmental changes. Results of micro- and macroscopic experiments showed that the existence of complex QS language "interpreter" ecosystems promote the stability maintenance of microbial community. Furthermore, a comprehensive kinetic computational model was developed for the optimization of tunable directed QSCN. Finally, the perspectives of the QSCN for the effective control of microbial communities were discussed and summarized. This study revealed the dynamic control of complex microbial communications, contributing to ecosystem-based engineering and microbiome-based therapeutics. [ABSTRACT FROM AUTHOR]

[Display omitted] • Synthetic microbial communities to guide food fermentations. • Complexity of fermented food microbiomes responsible for its stability and resilience. • Multi-disciplinary approaches necessary to build representative fermented food microbiomes. This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems. [ABSTRACT FROM AUTHOR]

The risk of pharmaceuticals and personal care products (PPCPs) has been paid more attention after the outbreak of COVID-19, threatening the ecology and human health resulted from the massive use of drugs and disinfectants. Wastewater treatment plants are considered the final stop to restrict PPCPs from wide spreading into the environment, but the performance of conventional treatment is limited due to their concentrations and characteristics. Previous studies have shown the unreplaceable capability of moving bed-biofilm reactor (MBBR) as a cost-effective method with layered microbial structure for treating wastewater even with toxic compounds. The biofilm community and microbial interactions are essential for the MBBR process in completely degrading or converting types of PPCPs to secondary metabolites, which still need further investigation. This review starts with discussing the initiation of MBBR formation and its influencing parameters according to the research on MBBRs in the recent years. Then the efficiency of MBBRs and the response of biofilm after exposure to PPCPs are further addressed, followed by the bottlenecks proposed in this field. Some critical approaches are also recommended for mitigating the deficiencies of MBBRs based on the recently published publications to reduce the environmental risk of PPCPs. Finally, this review provides fundamental information on PPCPs removal by MBBRs with the main focus on microbial interactions, promoting the MBBRs to practical application in the real world of wastewater treatment. [Display omitted] • Biofilm formation and characteristics were vital to the conventional nutrient and PPCPs removal in MBBRs. • Crucial parameters for biofilm formation and the removal of PPCPs were carefully discussed. • The microbial response of MBBR under the stress of PPCPs was investigated. • Coupled systems with MBBRs and other physiochemical methods were the new trend for enhancing PPCPs removal. • Further research should be conducted on the regulatory rules by QS for microbial interactions. [ABSTRACT FROM AUTHOR]

Fruit and vegetable waste (FVW) are characterized by high-water content. Solid-liquid separation of FVW by crushing-extrusion physical pre-treatment provides fruit and vegetable wastewater (FVWW), and then for anaerobic biological treatment to recover methane, which is considered a cost-effective approach. However, anaerobic treatment of FVWW faces difficulties with low methane productivity and over-accumulation of volatile fatty acids (VFAs). In this study, the expanded granular sludge bed (EGSB) reactor was used for the anaerobic treatment of FVWW and the regulatory strategy to alleviate over-acidification was proposed. When the influent chemical oxygen demand (COD) concentration was 10000 mg/L, the hydraulic retention time (HRT) was 2 days, the organic loading rate (OLR) reached 5 g COD/L/d, the maximum methane productivity reached 301.14 ± 2.32 mL/g COD with a COD removal rate of 96 % ± 2 %. Lower VFAs accumulation was observed when decreasing the influent COD concentration to the same OLR compared with extending HRT, resulting in 38.5 % higher methane productivity. Decreasing the influent COD concentration not only benefited the enrichment of acetogens and hydrogenotrophic methanogens but also specifically enriched syntrophic bacteria. The enhanced syntrophic acetogenesis and hydrogenotrophic methanogens maybe the main reasons for promoting the degradation of propionate and butyrate and improving the methane productivity. [Display omitted] [ABSTRACT FROM AUTHOR]

Triclocarban (TCC) and its metabolite, 3,4-dichloroaniline (DCA), are classified as emerging organic contaminants (EOCs). Significant concerns arise from water and soil contamination with TCC and its metabolites. These concerns are especially pronounced at high concentrations of up to approximately 20 mg/kg dry weight, as observed in wastewater treatment plants (WWTPs). Here, a TCC-degrading co-culture system comprising Rhodococcus rhodochrous BX2 and Pseudomonas sp. LY-1 was utilized to degrade TCC (14.5 mg/L) by 85.9% in 7 days, showing improved degradation efficiency compared with monocultures. A combination of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR) was performed. Meanwhile, through the combination of further experiments involving heterologous expression and gene knockout, we proposed three TCC metabolic pathways and identified four key genes (tccG , tccS , phB , phL) involved in the TCC degradation process. Moreover, we revealed the internal labor division patterns and connections in the co-culture system, indicating that TCC hydrolysis products were exchanged between co-cultured strains. Additionally, mutualistic cooperation between BX2 and LY-1 enhances TCC degradation efficiency. Finally, phytotoxicity assays confirmed a significant reduction in the plant toxicity of TCC following synergistic degradation by two strains. The in-depth understanding of the TCC biotransformation mechanisms and microbial interactions provides useful information for elucidating the mechanism of the collaborative biodegradation of various contaminants. [Display omitted] • An efficient degradation system for triclocarban was established by two bacterial strains. • The efficient degradation system degraded 85.9% of 14.5 mg/L TCC. • Further degradation of the intermediate 3, 4 - dichloroaniline from TCC was achieved. • The internal labor division was revealed by three metabolic pathways in the co-culture system. [ABSTRACT FROM AUTHOR]

Grapevine trunk diseases (GTDs) are currently among the most important health challenges for viticulture in the world. Esca, Botryosphaeria dieback, and Eutypa dieback are the most current GTDs caused by fungi in mature vineyards. Their incidence has increased over the last two decades, mainly after the ban of sodium arsenate, carbendazim, and benomyl in the early 2000s. Since then, considerable efforts have been made to find alternative approaches to manage these diseases and limit their propagation. Biocontrol is a sustainable approach to fight against GTD-associated fungi and several microbiological control agents have been tested against at least one of the pathogens involved in these diseases. In this review, we provide an overview of the pathogens responsible, the various potential biocontrol microorganisms selected and used, and their origins, mechanisms of action, and efficiency in various experiments carried out in vitro, in greenhouses, and/or in vineyards. Lastly, we discuss the advantages and limitations of these approaches to protect grapevines against GTDs, as well as the future perspectives for their improvement.

Chemical interactions have been shown to regulate several marine life processes, including selection of food sources, defense, behavior, predation, and mate recognition. These chemical communication signals have effects not only at the individual scale, but also at population and community levels. This review focuses on chemical interactions between marine fungi and microalgae, summarizing studies on compounds synthetized when they are cultured together. In the current study, we also highlight possible biotechnological outcomes of the synthetized metabolites, mainly for human health applications. In addition, we discuss applications for bio-flocculation and bioremediation. Finally, we point out the necessity of further investigating microalgae-fungi chemical interactions because it is a field still less explored compared to microalga–bacteria communication and, considering the promising results obtained until now, it is worthy of further research for scientific advancement in both ecology and biotechnology fields.

• The strategies of co-cultivation for metabolite production have been discovered. • The recent advancements and underlying mechanisms of co-cultivation were proposed. • The interactive cues and metabolic potential of co-cultivation were investigated. Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques. [ABSTRACT FROM AUTHOR]

Microbial interactions play an important role in initial cell adhesion and the endurance of biofilm toward disinfectant stresses. The present study aimed to evaluate the effect of microbial interactions on biofilm formation and the disinfecting activity of an innovative photocatalytic surfactant based on TiO2 nanoparticles. Listeria monocytogenes, Salmonella Enteritidis, Escherichia coli, Leuconostoc spp., Latilactobacillus sakei, Serratia liquefaciens, Serratia proteomaculans, Citrobacter freundii, Hafnia alvei, Proteus vulgaris, Pseudomonas fragi, and Brochothrix thermosphacta left to form mono- or dual-species biofilms on stainless steel (SS) coupons. The effectiveness of the photocatalytic disinfectant after 2 h of exposure under UV light on biofilm decontamination was evaluated. The effect of one parameter i.e., exposure to UV or disinfectant, was also determined. According to the obtained results, the microbial load of a mature biofilm depended on the different species or dual species that had adhered to the surface, while the presence of other species could affect the biofilm population of a specific microbe (p < 0.05). The disinfectant strengthened the antimicrobial activity of UV, as, in most cases, the remaining biofilm population was below the detection limit of the method. Moreover, the presence of more than one species affected the resistance of the biofilm cells to UV and the disinfectant (p < 0.05). In conclusion, this study confirms that microbial interactions affected biofilm formation and decontamination, and it demonstrates the effectiveness of the surfactant with the photocatalytic TiO2 agent, suggesting that it could be an alternative agent with which to disinfect contaminated surfaces.

Microbial interactions shape ecosystem diversity and chemistry through production and exchange of organic compounds, but the impact of regulatory mechanisms on production and release of these exometabolites is largely unknown. We studied the extent and nature of impact of two signaling molecules, tropodithietic acid (TDA) and the quorum sensing molecule acyl homoserine lactone (AHL) on the exometabolome of the model bacterium Phaeobacter inhibens DSM 17395, a member of the ubiquitous marine Roseobacter group. Exometabolomes of the wild type, a TDA and a QS (AHL-regulator) negative mutant were analyzed via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Based on a total of 996 reproducibly detected molecular masses, exometabolomes of the TDA and QS negative mutant were ∼70% dissimilar to each other, and ∼90 and ∼60% dissimilar, respectively, to that of the wild type. Moreover, at any sampled growth phase, 40–60% of masses detected in any individual exometabolome were unique to that strain, while only 10–12% constituted a shared "core exometabolome." Putative annotation revealed exometabolites of ecological relevance such as vitamins, amino acids, auxins, siderophore components and signaling compounds with different occurrence patterns in the exometabolomes of the three strains. Thus, this study demonstrates that signaling molecules, such as AHL and TDA, extensively impact the composition of bacterial exometabolomes with potential consequences for species interactions in microbial communities. [ABSTRACT FROM AUTHOR]

Candida albicans can coaggregate with Streptococcus gordonii and cocolonize in the oral cavity. Saliva provides a vital microenvironment for close interactions of oral microorganisms. However, the level of fermentable carbohydrates in saliva is not sufficient to support the growth of multiple species. Glycoside hydrolases (GHs) that hydrolyze glycoproteins are critical for S. gordonii growth in low-fermentable-carbohydrate environments such as saliva. However, whether GHs are involved in the cross-kingdom interactions between C. albicans and S. gordonii under such conditions remains unknown. In this study, C. albicans and S. gordonii were cocultured in heart infusion broth with a low level of fermentable carbohydrate. Planktonic growth, biofilm formation, cell aggregation, and GH activities of monocultures and cocultures were examined. The results revealed that the planktonic growth of cocultured S. gordonii in a low-carbohydrate environment was elevated, while that of cocultured C. albicans was reduced. The biomass of S. gordonii in dual-species biofilms was higher than that of monocultures, while that of cocultured C. albicans was decreased. GH activity was observed in S. gordonii, and elevated activity of GHs was detected in S. gordonii-C. albicans cocultures, with elevated expression of GHrelated genes of S. gordonii. By screening a mutant library of C. albicans, we identified a tec1D/D mutant strain that showed reduced ability to promote the growth and GH activities of S. gordonii compared with the wild-type strain. Altogether, the findings of this study demonstrate the involvement of GHs in the cross-kingdom metabolic interactions between C. albicans and S. gordonii in an environment with low level of fermentable carbohydrates. [ABSTRACT FROM AUTHOR]

The gut microbiota is associated with reproductive disorders in multiple ways. This research investigated possible differences in gut microbiome compositions between patients with uterine fibroids (UFs) and healthy control subjects in order to further provide new insight into its etiology. Stool samples were collected from 85 participants, including 42 UF patients (case group) and 43 control subjects (control group). The gut microbiota was examined with 16S rRNA quantitative arrays and bioinformatics analysis. The α-diversity in patients with UFs was significantly lower than that of healthy controls and negatively correlated with the number of tumorigeneses. The microbial composition of the UF patients deviated from the cluster of healthy controls. Stool samples from patients with UFs exhibited significant alterations in terms of multiple bacterial phyla, such as Firmicutes, Proteobacteria, Actinobacteria, and Verrucomicrobia. In differential abundance analysis, some bacteria species were shown to be downregulated (e. g., Bifidobacteria scardovii , Ligilactobacillus saerimneri , and Lactococcus raffinolactis) and upregulated (e. g., Pseudomonas stutzeri and Prevotella amnii). Furthermore, the microbial interactions and networks in UFs exhibited lower connectivity and complexity as well as higher clustering property compared to the controls. Taken together, it is possible that gut microbiota dysbiosis has the potential as a risk factor. This study found that UFs are associated with alterations of the gut microbiome diversity and community network connectivity. It provides a new direction to further explore the host–gut microbiota interplay and to develop management and prevention in UF pathogenesis. [ABSTRACT FROM AUTHOR]

Bacterial vaginosis (BV) is associated with serious gynaecologic and obstetric complications. The hallmark of BV is the presence of a polymicrobial biofilm on the vaginal epithelium, but BV aetiology is still a matter of debate. We have previously developed an in vitro biofilm model that included three BV-associated species, but, up to now, no studies are available whereby more bacterial species are grown together to better mimic the in vivo situation. Herein, we characterized the first polymicrobial BV biofilm consisting of six cultivable BV-associated species by using both in vitro and ex vivo vaginal tissue models. Both models revealed that the six species were able to incorporate the polymicrobial biofilm, at different bacterial concentrations. As it has been thought that this polymicrobial biofilm may increase the survival of BV-associated species when exposed to antibiotics, we also assessed if the Thymbra capitata essential oil (EO), which has recently been shown to be highly bactericidal against several Gardnerella species, could maintain its anti-biofilm activity against this polymicrobial biofilm. Under our experimental conditions, T. capitata EO exhibited a high antibacterial effect against polymicrobial biofilms, in both tested models, with a significant reduction in the biofilm biomass and the number of culturable cells. Overall, this study shows that six BV-associated species can grow together and form a biofilm both in vitro and when using an ex vivo model. Moreover, the data obtained herein should be considered in further applications of T. capitata EO as an antimicrobial agent fighting BV. [ABSTRACT FROM AUTHOR]

Planktonic microorganisms in aquatic ecosystems form complex assemblages of highly interactive taxa and play key roles in biogeochemical cycles. However, the microbial interactions within bacterial and microeukaryotic communities, and the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances in the river estuary remain unknown. Here, 16S and 18S rRNA gene sequencing were used to investigate the compositional changes and the co-occurrence patterns of bacterial and microeukaryotic communities. The results showed that the rare taxa in the bacterial communities were more prevalent than those in the microeukaryotic communities and may influence the resilience and resistance of microorganisms to environmental variations in estuarine ecosystems. The environmental variations had strong effects on the microeukaryotic communities and their assembly mechanisms but not on the bacterial communities in our studied area. However, based on co-occurrence network analyses, the bacterial communities had stronger links and more complex interactions than microeukaryotic communities, suggesting that bacterial networks may help improve the buffering capacities of the estuarine ecosystem against environmental change. The keystone taxa of bacteria mainly belonged to rare subcommunities, which further illustrates that rare taxa may play fundamental roles in network persistence. Overall, these results provide insights into the microbial responses of aquatic ecosystems to environmental heterogeneity. [ABSTRACT FROM AUTHOR]

Microbial mass spectrometry imaging (MSI) is a powerful tool used to generate biological hypotheses about the roles of metabolites in microbial competition based upon their two-dimensional spatial distribution. The most commonly used ionization method for microbial MSI is matrix-assisted laser desorption ionization (MALDI). However, medium components and microbial metabolites influence the adhesion of agar samples to the MALDI target, limiting the applicability of MALDI MSI to microbes grown on specific media. Here, we describe a three-step process using a robotic sprayer for a matrix application that improves the adherence of agar samples to the MALDI target, enabling the use of different media for microbial growth and an MSI analysis of larger sample surface areas. [ABSTRACT FROM AUTHOR]

Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future.

Diversity and compositional analysis are the most common approaches in deciphering microbial community differences. However, these approaches neglect microbial structural differences driven by microbial interactions. In this study, the microbiota data were generated from 12 rectal digesta samples collected from steers in which the Shiga toxin 2 gene (stx2) was not expressed (defined as Stx2− group) in the bacteria, and those with stx2 expressed (defined as Stx2+ group) and used to explore whether microbial networks affect gut microbiota and foodborne pathogen virulence in cattle. Although the Shannon and Chao1 indices of rectal digesta microbial communities did not differ between the two groups (P > 0.05), 24 and 13 taxa were identified to be group-specific genera for Stx2− and Stx2+ microbial communities, respectively. The network analysis indicated 12 and 14 generalists (microbes that were densely connected with other taxa) in microbial communities for Stx2− and Stx2+ groups, and 8 out of 12 generalists and 6 out of 14 generalists were designated to Stx2− and Stx2+ group-specific genera, respectively. However, the 66 core genera were not classified as network generalists. Natural connectivity measurements revealed that the higher stability of the Stx2− microbial network in comparison to the Stx2+ network, suggesting that the structure of each microbial community was inherently different even when their diversity and composition were comparable. Group-specific genera intensely interacted with other taxa in the co-occurrence network, indicating that characterizing microbial networks together with group-specific genera could be an alternative approach to identify variation in microbial communities.

Investigation of drug-microbial interactions has gained prominence due to the increasing need to study pharmacomicrobiomics. Previous research has revealed the microbiome's role in drug metabolism, influencing efficacy, bioavailability, and toxicity. Several potential interactions have reported between drugs and microbes, including bioaccumulation, biotransformation, and the influence of drugs on microbial growth. To facilitate the investigation of drug-microbial interactions, in this study, we present an integrated platform and procedure for investigating drug-microbial interactions, focusing on biotransformation, bioaccumulation, metabolomics, exometabolomics, lipidomics, and exolipidomics. To illustrate the feasibility of this platform, we examined the interactions between digoxin and Lactiplantibacillus pentosus (L. pentosus), revealing previously unknown interactions. Although the growth of L. pentosus was unaffected by digoxin, metabolomics, exometabolomics, lipidomics, and exolipidomics analyses revealed digoxin's impact on metabolites and lipids inside and outside L. pentosus. Additionally, we utilized a validated liquid chromatography-mass spectrometry quantification platform to evaluate digoxin biotransformation and bioaccumulation levels by L. pentosus. After accurately quantifying digoxin in the supernatant and pellet, we determined that approximately 8.7 % of digoxin was biotransformed by L. pentosus. Exolipidomics analysis further supported digoxin biotransformation, identifying digoxigenin and its metabolites. These findings elucidate the potential impact of L. pentosus on digoxin metabolism, underscoring the importance of considering microbial interactions in pharmacological research. We anticipate that the integrated platform could assist in more pharmacomicrobiomics studies and uncover unknown drug-microbial interactions., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Hsiao-Wei Liao reports financial support was provided by Ministry of Science and Technology of Taiwan. Hsiao-Wei Liao reports a relationship with Ministry of Science and Technology of Taiwan that includes: funding grants., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Bacterial-fungal interaction (BFI) is found ubiquitously and plays important roles in various environmental settings, thus being responsible for numerous biophysical and chemical processes in nature. In terms of BFI, the capacity of the bacterium to enhance the growth of fungal mycelia is an indication of the roles of the bacterium in mutualistic interaction, since increasing mycelial growth results in higher changes for fungal establishment. In this review, the interaction between mycelial growth-promoting bacterium (MGPB) and its fungal counterpart in agricultural settings and the promotion of mycelial growth as an outcome of mutual interactions in various environmental niches were evaluated. The beneficial relationships included endohyphal interaction, association of bacteria with mushrooms, bacteria-mycorrhizae symbiosis, and geomicrobiology. Furthermore, the mode of interaction between MGPB and their fungal counterparts was also explained. There are two fundamental modes of interaction involved, namely physical interaction and chemical interaction. The first involved endosymbiosis and bacterial attachment, while the latter comprised quorum sensing, volatile metabolites, enzymatic activity, and chemotaxis. Particularly, the growth stimulants secreted by the bacteria, which promote the growth of hyphae, are discussed thoroughly. Moreover, the chance of trade-off metabolites between fungi and their MGPBs as a consequence of mutualistic interaction will also be observed. Finally, the agricultural relevance of BFI, particularly the relation between fungi and MGPBs, will also be provided, including key technologies and future bioprospects for optimum application., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Competition phenomenon is widely presented in nature, however, few reports on the competition phenomenon between bacteria based on the perspective of quorum sensing (QS), especially between Gram-positive bacteria. Here, the Gram-positive bacteria Rhodococcus sp. HD1 and Microbacterium sp. HM-2 were co-cultured, and the epiphysiological indicators, transcriptomics combined with gene engineering technique were applied to clarify the role of QS in the competition between Gram-positive bacteria. The results showed that the morphology of strain HD1 was changed into ellipsoids from long rods, the surface-to-volume ratio increased, and the competition index increased within strains HM-2 and HD1. The biomass of strain HD1(8.06×10 7 CFU/mL) was decreased significantly (p＜0.05) under co-culture system, compared with mono-culture (5.75×10 8 CFU/mL), indicating that strain HM-2 had an inhibitory effect on HD1 at 12 h. Transcriptomic analysis revealed that QS-related genes were highly expressed in strain HM-2, and the expression level of the virulence gene TM&#95;0352 was the highest (FPKM: 1774.19). Meanwhile, the ABC transporters-related genes in strain HD1 were significantly increased. Furthermore, QS pathway-related genes in strain HM-2 and ABC transporters-related genes in strain HD1 showed a significant correlation with the gene TM&#95;0352 expression by the Mantel test analysis (p<0.05), surmising that the TM&#95;0352 gene played a dominant role in the co-culture system. Knockout and complementation experiments confirmed that the function of gene TM&#95;0352. The structural equation model showed that the QS up-regulation of strain HM-2 significantly promoted the expression of virulence genes, while strain HD1 promoted ABC transporters to cope with the up-regulation of TM&#95;0352. The up-regulation of TM&#95;0352 promoted the biomass of strain HM-2 and inhibited the biomass of HD1.The above results displayed that the competition phenomenon appeared by QS driving the up-regulation of TM&#95;0352 gene in strain HM-2, which led to the up-regulation of ABC transporters in strain HD1. And these findings provided new insights into the perspective of factors related to competition inhibition between bacteria., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

ABSTRACT Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of “rare” actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions. IMPORTANCE Many antibiotics were originally discovered from microbes. However, in recent decades, resistance to current treatments has risen, while novel antibiotic discovery has become increasingly challenging. Thus, there is a need to develop new strategies to find novel antimicrobials. Here, we incorporated three levels of innovation into a single, simple discovery pipeline: focusing on understudied bacteria with a high potential for producing antibiotics, growing these bacteria in binary microbial interactions, and screening for activity against a multidrug-resistant bacterium. This led us to discover a family of antimicrobials that we call the dynaplanins, which are synthesized by genes that were not detected by typical prediction algorithms. We found that dynaplanins likely block the function of one of three related enzymes called 2-oxo acid dehydrogenases, which are vital to cellular metabolism. Overall, our strategy based on bacterial competition led to discovery of a novel antibiotic that inhibits the ability to metabolize nutrients.

Bacterial vaginosis (BV) is associated with serious gynaecologic and obstetric complications. The hallmark of BV is the presence of a polymicrobial biofilm on the vaginal epithelium, but BV aetiology is still a matter of debate. We have previously developed an in vitro biofilm model that included three BV-associated species, but, up to now, no studies are available whereby more bacterial species are grown together to better mimic the in vivo situation. Herein, we characterized the first polymicrobial BV biofilm consisting of six cultivable BV-associated species by using both in vitro and ex vivo vaginal tissue models. Both models revealed that the six species were able to incorporate the polymicrobial biofilm, at different bacterial concentrations. As it has been thought that this polymicrobial biofilm may increase the survival of BV-associated species when exposed to antibiotics, we also assessed if the Thymbra capitata essential oil (EO), which has recently been shown to be highly bactericidal against several Gardnerella species, could maintain its anti-biofilm activity against this polymicrobial biofilm. Under our experimental conditions, T. capitata EO exhibited a high antibacterial effect against polymicrobial biofilms, in both tested models, with a significant reduction in the biofilm biomass and the number of culturable cells. Overall, this study shows that six BV-associated species can grow together and form a biofilm both in vitro and when using an ex vivo model. Moreover, the data obtained herein should be considered in further applications of T. capitata EO as an antimicrobial agent fighting BV.

The gut microbiota is associated with reproductive disorders in multiple ways. This research investigated possible differences in gut microbiome compositions between patients with uterine fibroids (UFs) and healthy control subjects in order to further provide new insight into its etiology. Stool samples were collected from 85 participants, including 42 UF patients (case group) and 43 control subjects (control group). The gut microbiota was examined with 16S rRNA quantitative arrays and bioinformatics analysis. The α-diversity in patients with UFs was significantly lower than that of healthy controls and negatively correlated with the number of tumorigeneses. The microbial composition of the UF patients deviated from the cluster of healthy controls. Stool samples from patients with UFs exhibited significant alterations in terms of multiple bacterial phyla, such as Firmicutes, Proteobacteria, Actinobacteria, and Verrucomicrobia. In differential abundance analysis, some bacteria species were shown to be downregulated (e.g., Bifidobacteria scardovii, Ligilactobacillus saerimneri, and Lactococcus raffinolactis) and upregulated (e.g., Pseudomonas stutzeri and Prevotella amnii). Furthermore, the microbial interactions and networks in UFs exhibited lower connectivity and complexity as well as higher clustering property compared to the controls. Taken together, it is possible that gut microbiota dysbiosis has the potential as a risk factor. This study found that UFs are associated with alterations of the gut microbiome diversity and community network connectivity. It provides a new direction to further explore the host–gut microbiota interplay and to develop management and prevention in UF pathogenesis.

Summary: Parasite-derived PVM-resident proteins are critical for complete parasite development inside hepatocytes, although the function of most of these proteins remains unknown. Here, we show that the upregulated in infectious sporozoites 4 (UIS4) protein, resident at the PVM, interacts with the host cell actin. By suppressing filamentous actin formation, UIS4 avoids parasite elimination. Host cell actin dynamics increases around UIS4-deficient parasites, which is associated with subsequent parasite elimination. Notably, parasite elimination is impaired significantly by the inhibition of host myosin-II, possibly through relieving the compression generated by actomyosin complexes at the host-parasite interface. Together, these data reveal that UIS4 has a critical role in the evasion of host defensive mechanisms, enabling hence EEF survival and development.

B-vitamins are essential micronutrients for marine plankton. Additionally, we now know many marine plankton cannot synthesize B-vitamins de novo (from scratch) and thus are reliant on external supplies. Details of B-vitamin exchange, whether ‘active’ or ‘passive’ (i.e. through cell secretion or mortality), are lacking and as a result we struggle to predict microbial physiology, community composition and biogeochemistry. We argue that significant advances in understanding of the impact of B-vitamin exchange and cycling on marine community structure and biogeochemistry can be made by focusing on unknowns related to the ‘in’s and out’s’ of B-vitamin transport, exchange between plankton, and ecosystem scale processing/transformation of B-vitamins. We point out that it is particularly necessary to reach beyond traditional categorization of populations as B-vitamin auxotrophs (requiring supplied vitamin) or prototrophs (de novo vitamin synthesizers) and begin addressing which populations are net ‘providers’ and/or ‘consumers’. This is a particularly interesting problem as organisms cannot be confidently categorized as net ‘providers’ and/or ‘consumers’ based on genome-based prediction, and it is possible the two roles may change over time and environmental conditions. We posit that greater knowledge of B-vitamin exchange, e.g. cross-feeding, acquisition and secretion systems, environmental triggers of ‘provision’ and ‘consumption’, will reveal unforeseen networking and novel niches across marine planktonic communities. Last, we advocate for further experiments tracking the responses of isolates or natural communities relative to vitamin availability, tracing flow of B-vitamins between cells using novel approaches (e.g. isotopic, fluorometric), and greater consideration of altered B-vitamin exchange and cycling under future climate scenarios.