FEMS microbes最新文献

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.

Toxoplasma gondii, an obligate intracellular parasite, acquires host nutrients to sustain its intracellular replication. A key interaction involves host mitochondrial association (HMA) with the parasitophorous vacuole membrane, previously thought to be strain- and cell-type-dependent, and notably absent in type 2 strains in fibroblasts. Here, we report that in human skeletal muscle KD3 myotubes, all three archetypal T. gondii strains-including type 2-demonstrate significant HMA. This association was confirmed by mitotracker staining and transmission electron microscopy. Notably, HMA appears to correlate inversely with the parasite's uptake of exogenous ¹³C-labeled fatty acids, suggesting a competitive nutrient environment shaped by host mitochondrial proximity. These findings highlight host cell-type specificity in mitochondrial interactions and suggest that HMA may function as a modulator of nutrient acquisition in a context-dependent manner. This work revises the understanding of strain-specific HMA and underscores the complexity of host-parasite metabolic interactions in muscle tissue, a physiologically relevant niche for chronic T. gondii infection.

Klebsiella pneumoniae is a critical pathogen often associated with multidrug resistance and hypervirulence. We report the isolation and characterization of three distinct lytic bacteriophages-Spear, Loop, and Shorty-from sewage, using a hypervirulent, hypermucoid K. pneumoniae K1 ST23 strain as the host. Despite genomic and structural differences, all three phages exhibited a narrow host range, infecting only the K1 serotype. Transmission electron microscopy and genomic analyses confirmed their lytic lifestyle and classifications: Spear and Loop are siphovirus-like, while Shorty is podovirus-like. A key focus was phage-host interaction and receptor usage. DNA sequence analysis showed no homology between the receptor-binding proteins, yet structural modelling revealed high similarity between Loop and Shorty tail fibers, aligning within a K1-specific lyase domain, suggesting phage genetic mosaicism. All three phages rely on capsular polysaccharide (CPS) for infection. Resistance selection under phage pressure yielded non-mucoid mutants, characteristic of CPS loss. Cross-resistance and adsorption assays confirmed CPS-dependence. Loop and Shorty showed near-complete loss of binding; Spear retained partial binding, suggesting additional receptors. These results highlight that unrelated phages can target the same bacterial structure, CPS. This has important implications for rational phage cocktail design, as CPS mutations may undermine seemingly diverse phage combinations.

Listeria monocytogenes is a food-borne pathogen that can cause severe disease in immunocompromised persons, and its ability to survive stressors encountered in food production environments (FPEs) makes it difficult to eliminate from the food chain. Previous transcriptomic analysis revealed that in response to lactic acid exposure, L. monocytogenes significantly upregulates Rli47, a noncoding RNA that has previously been shown to interact with the ilvA transcript and suppress growth of L. monocytogenes in the absence of isoleucine. We show that at logarithmic phase, an rli47 deletion mutant had a higher survival compared to the parent strain after exposure to lactic acid. Flow cytometry indicated that lactic acid exposure did not differentially affect the proportion of metabolically active cells in the deletion mutant and wild type. Transcriptomic analysis and in silico target prediction suggested that Rli47 could affect pathways involved with cell envelope structure; due to the link between cell envelope integrity and organic acid stress, it is possible that in the absence of rli47 the cell envelope of logarithmic phase L. monocytogenes cells is more resistant to lactic acid exposure. These results suggest that Rli47 functionality may vary due to factors including temperature and nutrient availability.

Interactions between viruses and sub-inhibitory concentrations of surfactants in water systems are understudied. At concentrations below the minimum inhibitory concentration (MIC), surfactants may interact with virus surface proteins without virus inactivation and alter virus surface properties. This study determined the MIC of benzyldimethyldodecylammonium chloride (BAC) and sodium dodecyl sulfate (SDS) on human adenovirus (ADV, non-enveloped, dsDNA) and mouse hepatitis virus (MHV, enveloped, ssRNA), and how sub-MIC surfactants influence virus isoelectric point (IEP), hydrated diameter, and interact with virus surface proteins. Both surfactants had MICs of 1 mg/L over 60 minutes. Experimental IEPs were lower than IEPs estimated based on amino acid structures. The ADV IEP was 3.8 without surfactants and dropped to 3.3 with BAC and lower than 3 with SDS. The MHV IEP was 4.2 without surfactants and decreased to 4.1 with SDS and 3.4 with BAC. Dynamic light scattering showed SDS and BAC decreased ADV hydrated diameter from 142 ± 8 nm (no surfactant) to 109-116 nm, while MHV decreased from 150 ± 10 nm (no surfactants) to 132-140 nm upon surfactant exposure. Molecular dynamics simulations revealed that SDS, due to its multivalent sulfate headgroup, forms numerous intimate contacts with the MHV spike protein that markedly perturb its electrostatic environment. In contrast, BAC engages only sporadically and diffusely with the protein, indicating a much weaker influence on its structure and electrostatics. Overall, this study showed that ionic surfactants can influence virus properties thus altering virus interactions with surfaces in engineered and natural systems.

Gram-negative bacteria can use type III secretion systems to inject effector proteins into eukaryotic target cells. Most effectors are co-expressed with specific chaperone proteins that are required for the secretion of their cognate effector. Although chaperones share characteristics across species, no common mechanism of action has been identified. In particular, it remains unclear, if and how chaperones target effectors to the type III secretion injectisome. In this study, we analyzed the interaction network, cellular localization, mobility, and function of SycH and SycE, two Yersinia enterocolitica T3SS chaperones, in live bacteria. While both chaperones strongly interacted with their cognate effectors, SycH additionally bound two negative regulators, YscM1/2, whereas SycE consistently showed weak interactions and proximity to various other effectors. In contrast, the chaperones did not specifically interact with the injectisome or the cytosolic T3SS components that were recently found to shuttle effectors to the injectisome. Mobility measurements and single particle tracking support these findings. Taken together, our results indicate a handover of the effector YopH from its chaperone SycH to the shuttle complexes in the bacterial cytosol and raise the possibility that a similar mechanism applies to other effector/chaperone pairs .