FEMS microbes最新文献

Fermented foods represent complex microbial ecosystems that contribute to food quality, functionality, and potential health benefits, yet many traditional fermented foods remain poorly characterized. The aim of this study was to study microbial diversity, and functional potential of underexplored traditional Indonesian fermented food. The fermented products displayed substantial variation in bacterial richness, ranging from 65 to 614 bacterial amplicon sequence variants across samples. The microbial communities were dominated by bacterial taxa affiliated with the orders Bacillales and Lactobacillales, alongside fungal taxa from the order Mucorales. The plant-based products i.e. tape ketan and tape singkong had a higher bacterial abundance but lower diversity than animal-based terasi. We found significant correlations between bacterial and fungal communities dominated by positive cooccurrence patterns and highly complex networks especially in terasi. Each food product was characterized by a unique functional profile of genes linked to beneficial metabolic functions (biosynthesis of bacteriocins, short-chain fatty acids, and vitamins) but tape ketan samples demonstrated the highest diversity and abundance of them. Metagenome assembled genomes reflect a high diversity of health beneficial properties as well as substrate-specific degradation capabilities. Traditional Indonesian fermented foods harbour functionally redundant but phylogenetically diverse taxa offering a potential source for probiotic traits and functional food development.

Studies in model organisms and wild populations have uncovered manifold links between the gut microbiome and sociality, which, considering the adaptiveness of social behaviour, suggest a potentially generalized coevolution between microbiomes and social behaviour. Here, we leverage phylogenetically and ecologically diverse data from the Earth Microbiome Project to test the generality of the links between sociality and the gut microbiome in wild animals. We find evidence of a small but significant link between sociality and microbiome beta diversity, but not alpha diversity, in mammalian taxa, potentially due to socially mediated microbial transmission. Our work highlights the value of leveraging large-scale multi-study datasets to test fundamental questions about the role of sociality in host-microbiome coevolution.

The intra-tumoural microbiome is an increasing area of research with potential benefits in cancer diagnostics and treatment development. Numerous studies have implicated Fusobacterium nucleatum, a member of the oral microbiota, in the development, immune evasion, and dissemination of oral and colorectal tumours. Although F. nucleatum is yet to be classified as a cause or consequence of cancer, reports indicate the microorganism's involvement in DNA damage, pathologic glucose uptake, and cellular proliferation. This accumulation of genetic instability is consistent with the multistep nature of malignant neoplasm progression. Virulence factors of F. nucleatum were shown to maintain an unresolved inflammatory state and impair the normal function of immune cells. The accompanying pro-inflammatory conditions facilitate vasculature remodelling, expediting tumour expansion, through a range of mechanisms. Pro-metastatic epithelial-to-mesenchymal transition and changes in gene expression have been observed in cancer cells upon F. nucleatum infection, suggesting an association with poorer prognosis. As a frequently encountered microorganism in the oral and colorectal intra-tumoural microbiome, F. nucleatum represents an intriguing, yet cautious research prospect with opportunities for novel prevention and therapeutic strategies. The objective of this work is to review the relevant evidence, taking into account the complexity of the tumour microenvironment.

Radiation resistance in Deinococcus requires an SOS-independent response mechanism, controlled by M78 family (COG2856) metallopeptidase IrrE and XRE family transcriptional repressor DdrO, to induce expression of DNA repair genes after exposure to radiation. DdrO must form dimers to bind target DNA sites. IrrE inactivates DdrO by cleaving the C-terminal dimerization domain of DdrO. However, the molecular basis of the interaction between IrrE and DdrO is still unknown. Here, we showed that IrrE is monomeric in solution and forms heterodimers with DdrO, with the N-terminal DNA-binding domain of DdrO contributing to the interaction. We further revealed that the initially isolated radiation-sensitive irrE mutant strain encodes an oxidation-sensitive IrrE protein affected in DdrO cleavage. Predicted COG2856/XRE regulatory protein pairs are present in many environmental, pathogenic, and industrial bacteria. Single-stranded DNA enhanced the cleavage activity of IrrE from Deinococcus as well as from closely related Marinithermus and Oceanithermus species, but not of the distant homologs ImmA from Bacillus subtilis and Rir from Streptococcus thermophilus. The formation of a heterotrimer containing IrrE, DdrO, and single-stranded DNA was also demonstrated. Together, these findings provide new insights into the molecular interplay between the key regulators IrrE and DdrO.

Drug combinations offer one potential strategy for slowing the evolution of antibiotic resistance. In this work, we investigate the evolution of drug resistance (strictly, the decrease in susceptibility) in populations of Enterococcus faecalis, an opportunistic human pathogen, exposed to different concentrations of the rarely used combination of linezolid (LZD) and levofloxacin (LEV). Using continuous culture bioreactors, we measured the two-dimensional dose-response surface of ancestral populations of E. faecalis, revealing that the LZD-LEV combination is strongly antagonistic, resulting in increased growth as LZD concentration is increased at a (sufficiently high) fixed concentration of LEV. Next, we performed multiday (50+ hour) evolution experiments by continually exposing populations to four different fixed-concentration combinations and then characterized isolates from adapted populations using whole genome sequencing and phenotypic dose-response curves. To control for differences in inhibition levels for different concentration combinations, we chose LZD-LEV combinations that fall along a single contour of constant growth in the two-drug space of LZD-LEV concentrations. Despite similar levels of initial inhibition across the four concentration combinations, we found that adaption is markedly different, with the most rapid adaptation and highest levels of evolved resistance occurring at combinations that include a high concentration of one drug and low concentration of the other. By contrast, we found almost no adaptation when both drugs were used at high concentrations, an initially surprising result that can be explained by simple drug-rescaling arguments applied to the antagonistic dose-response surface. Our results underscore the potential utility of a nonstandard (and strongly antagonistic) drug combination in suppressing resistance.

Phototrophic microorganisms can produce all colors in the light spectrum, becoming pivotal players in implementing sustainable color biomanufacturing technologies from CO₂ utilization. This review compiles information on metabolism and applications of phototrophic microorganisms relevant to the production of several valuable pigments. First, a comparative network analysis of the biological functions of oxygenic (OPs) and anoxygenic (APs) phototrophs was generated based on their pigment metabolism, while considering 19 taxonomic phyla, including microalgae, bacteria, bacterial endosymbionts, and archaea. Overall, the assessment comprised 84 pigments from 47 OPs subgroups and 68 pigments from 23 APs subgroups. The recent update of the nomenclature for cyanobacteria, microalgae, phototrophic bacteria, and phototrophic archaea has improved our understanding of carotenoids, phycobiliproteins, and microbial sunscreens, with applications as food ingredients, cosmetics, and engineered materials with enhanced functionalities. Second, this manuscript presents recent advances in bioprocess engineering, systems biology, and artificial intelligence to overcome challenges hindering economic feasibility at the industrial level. For example, culturing, extraction, and purification techniques, combined with model-driven methodologies, can nearly double pigment productivity, thereby accelerating biomass growth rates. These achievements have enabled rapid and reliable pigment identification and quantification, providing a thorough analysis that tackles critical aspects to enhance progress on sustainable color production.

Within the past ten years, genetic evidence has been increasing for the direct role that microbes play in microbiologically influenced corrosion (MIC), also known as biocorrosion or biodeterioration. One prominent example is the correlation between the corrosion of metal and the presence of genes encoding an extracellular [NiFe]-hydrogenase (MIC hydrogenase) in the methanogenic archaeon, Methanococcus maripaludis. In this study, DNA sequencing and bioinformatic analysis were used to classify the MIC hydrogenase as belonging to a core set of genes, the MIC core, found so far in Methanococci and Methanobacteria classes of methanogens. Genetic evidence is provided for the mobilization of the MIC core via multiple mechanisms, including a horizontal gene transfer event from Methanobacteria to Methanococci and a newly described MIC-transposon. A detailed comparison of M. maripaludis genomes further pointed to the relevance that cell wall modifications involving N-glycosylation of S-layer proteins and the MIC hydrogenase likely play in methanogen-induced MIC (Mi-MIC). Microscopic analysis of corrosive methanogens encoding the MIC core indicated that Methanobacterium-affiliated strain IM1 can form extensive biofilms on the surface of corrosion products whereas individual cells of M. maripaludis Mic1c10 were only found localized to crevices in the corrosion layer. An updated model of Mi-MIC involving two modes of action is presented, which predicts that the propensity of cells to adhere to iron surfaces directly influences the rate of corrosion due to the localization of the MIC hydrogenase at the metal-microbe interface.

Recently, it has been reported that either infection of rodents with the periodontopathogenic Porphyromonas gingivalis (Pg) or administration of its lipopolysaccharide (Pg-LPS) to rodents with non-alcoholic steatohepatitis (NASH) causes progression and exacerbation of the disease. Thus, periodontal disease and NASH are closely related, and further research is required. Medaka (Oryzias latipes) has been used as an alternative model for studying human diseases in rodents. In this study, we investigated the association between NASH and Pg-LPS in a NASH model medaka, fed a high-fat diet for 12 weeks, and then injected intraperitoneally with Pg-LPS (low-dose Pg-LPS group: 1.5 mg/kg, high-dose Pg-LPS group: 15 mg/kg) once a week from 5 to 8 weeks. After 12 weeks, the effects of Pg-LPS administration on NASH pathology were evaluated. As a result, liver weight and liver weight/body weight values tended to be higher in the high-dose Pg-LPS group compared to the other groups. HE and Oil Red O staining of the liver showed increased fat accumulation with high-dose Pg-LPS. In addition, Sirius red staining of the liver found fibrosis only in the high-dose Pg-LPS group. These results suggest that Pg-LPS administration may accelerate the progression of the disease in the NASH model medaka.

The deep sea is a largely unexplored extreme environment supporting a diverse biological community adapted to low temperatures and high pressures. Such environments support microbial life that may be a source of novel antibiotics and other drugs. Whilst this is often the case, many species with bioactive capabilities may be missed with traditional culturing methods. In this study, a total of 16 different concentrations and types of media were employed, to culture 389 bacterial isolates using Dilution to Extinction methods and Actinobacteria Directed Cultivation techniques. This generated 72 (18.6%) isolates with narrow and broad-spectrum activity against ESKAPE pathogens including Escherichia coli (E. coli), methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococci. We also report that an early-stage 'One Strain Many Compounds' approach can reveal a greater number of bioactive isolates that otherwise would have been missed; 12 isolates initially deemed 'inactive' were seen to exhibit activity towards S. aureus and/or E. coli. We emphasize the importance of a thorough initial screening method to capture bioactive isolates and show how selecting only morphologically distinct isolates for screening may result in species with promising bioactivity being overlooked. Our findings justify on-going investigation of Pheronema sponges for bioactive microbiota.

Members of the genus Janthinobacterium are widespread and found in soil and freshwater ecosystems, but also in the skin of humans, fish, and amphibians. They are known for producing violacein, and they typically have antifungal properties. In amphibians, Janthinobacterium spp. protect their hosts against fungal infections. We examined the diversity of five Janthinobacterium strains isolated from the skin and rearing water of Atlantic salmon fry by phenotypic characterization and comparative genomics. Although their 16S rRNA gene sequences were almost identical, their phenotypes were highly dissimilar, and only two of the species consistently produced violacein. Genomic analyses revealed that they represented five species, and phylogenetic analysis suggested that only one was closely related to a previously described species (Janthinobacterium tructae ^T). All strains possessed the Janthinobacterium quorum sensing system, while three harbored genes of the AHL QS system. They had great potential for producing secondary metabolites, and one carried putative genes of the antibiotic tropodithietic acid, previously described in the marine Phaeobacter. Interestingly, they all carried putative genes for heterotrophic carbon fixation. Furthermore, they had the genetic potential for chemotaxis and motility; compatible with a host-associated lifestyle. Gnotobiotic experiments confirmed that they were able to colonize yolk sac fry of Atlantic salmon.