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Frontiers in Microbiology 2023The gut microbiota, a complex ecosystem integral to host wellbeing, is modulated by environmental triggers, including exposure to heavy metals such as chromium. This...
The gut microbiota, a complex ecosystem integral to host wellbeing, is modulated by environmental triggers, including exposure to heavy metals such as chromium. This study aims to comprehensively explore chromium-induced gut microbiota and metabolomic shifts in the quintessential lepidopteran model organism, the silkworm (). The research deployed 16S rDNA sequence analysis and LC/MS metabolomics in its experimental design, encompassing a control group alongside low (12 g/kg) and high (24 g/kg) feeding chromium dosing regimens. Considerable heterogeneity in microbial diversity resulted between groups. emerged as potentially resilient to chromium stress, while elevated Propionibacterium was noted in the high chromium treatment group. Differential analysis tools LEfSe and random forest estimation identified key species like like and , offering potential avenues for bioremediation. An examination of gut functionality revealed alterations in the KEGG pathways correlated with biosynthesis and degradation, suggesting an adaptive metabolic response to chromium-mediated stress. Further results indicated consequential fallout in the context of metabolomic alterations. These included an uptick in histidine and dihydropyrimidine levels under moderate-dose exposure and a surge of gentisic acid with high-dose chromium exposure. These are critical players in diverse biological processes ranging from energy metabolism and stress response to immune regulation and antioxidative mechanisms. Correlative analyses between bacterial abundance and metabolites mapped noteworthy relationships between marker bacterial species, such as and , and specific metabolites, emphasizing their roles in enzyme regulation, synaptic processes, and lipid metabolism. Probiotic bacteria showed robust correlations with metabolites implicated in stress response, lipid metabolism, and antioxidant processes. Our study reaffirms the intricate ties between gut microbiota and metabolite profiles and decodes some systemic adaptations under heavy-metal stress. It provides valuable insights into ecological and toxicological aspects of chromium exposure that can potentially influence silkworm resilience.
PubMed: 37954243
DOI: 10.3389/fmicb.2023.1278271 -
ACS Omega Oct 2023The objective of this study was to investigate the impact of thermophilic bacteria on crude fiber content, carbohydrate-active enzyme (CAZyme) genes, and associated...
The objective of this study was to investigate the impact of thermophilic bacteria on crude fiber content, carbohydrate-active enzyme (CAZyme) genes, and associated microbial communities during Chinese medicine residues composting. The study examines changes over 15 days of composting with () and without (CK) thermophilic microbial agents. Results show that the group compost temperature reached a maximum of 71.0 °C and remained above 70 °C for 2 days, while the group CK maximum temperature was only 60.9 °C. On Day 15, the seed germination index (GI) of group reached 98.7%, while the group CK GI was only 56.7%. After composting, the degradation rates of cellulose, hemicellulose, and lignin in group increased by 5.1, 22.5, and 18.5%, respectively, compared to those in group CK. Thermophilic microbial agents changed the microbial communities related to CAZymes, increasing and abundance and reducing and abundance. Thermophilic microbial agents also increased the abundance of the GT4, GT2_Glycos_transf_2, and AA3 gene families. These results show that thermophilic microbial agents can increase composting temperature, accelerate compost maturation, and promote crude fiber degradation. Therefore, they have broad application potential.
PubMed: 37901486
DOI: 10.1021/acsomega.3c05442 -
STAR Protocols Dec 2023Protein-protein interactions are foundational for many cellular processes. Such interactions are especially challenging to identify if they are transient or depend on...
Protein-protein interactions are foundational for many cellular processes. Such interactions are especially challenging to identify if they are transient or depend on environmental conditions. This protocol details steps to identify stable and transient protein interactomes in the bacterium Myxococcus xanthus using biotin ligase miniTurbo-based proximity labeling. We include instructions for optimizing the expression of control proteins, in vivo biotin labeling of bacteria grown on a surface or in suspension culture, enrichment of biotinylated proteins, and sample processing for proteomic analysis. For complete details on the use and execution of this protocol, please refer to Branon et al. (2018)..
Topics: Biotin; Myxococcus xanthus; Proteomics
PubMed: 37883223
DOI: 10.1016/j.xpro.2023.102657 -
MBio Oct 2023Type IVa pili (T4aP) are widespread bacterial cell surface structures with important functions in motility, surface adhesion, biofilm formation, and virulence. Different...
Type IVa pili (T4aP) are widespread bacterial cell surface structures with important functions in motility, surface adhesion, biofilm formation, and virulence. Different bacteria have adapted different piliation patterns. To address how these patterns are established, we focused on the bipolar localization of the T4aP machine in the model organism by studying the localization of the PilQ secretin, the first component of this machine that assembles at the poles. Based on experiments using a combination of fluorescence microscopy, biochemistry, and computational structural analysis, we propose that PilQ, and specifically its AMIN domains, binds septal and polar peptidoglycan, thereby enabling polar Tgl localization, which then stimulates PilQ multimerization in the outer membrane. We also propose that the presence and absence of AMIN domains in T4aP secretins contribute to the different piliation patterns across bacteria.
Topics: Fimbriae Proteins; Myxococcus xanthus; Fimbriae, Bacterial
PubMed: 37754549
DOI: 10.1128/mbio.01593-23 -
MSystems Oct 2023Understanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these...
Understanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these multicellular communities, various cues can trigger differentiation into distinct cell types, allowing cells to adapt to their specific local environment. The soil bacterium forms biofilms in response to starvation, marked by cells aggregating into mounds. Some aggregates persist as spore-filled fruiting bodies, while others disperse after initial formation for unknown reasons. Here, we use a combination of cell tracking analysis and computational simulations to identify behaviors at the cellular level that contribute to aggregate dispersal. Our results suggest that cells in aggregates actively determine whether to disperse or persist and undergo a transition to sporulation based on a self-produced cue related to the aggregate size. Identifying these cues is an important step in understanding and potentially manipulating bacterial cell-fate decisions.
Topics: Spores, Bacterial; Myxococcus xanthus; Biofilms; Cell Differentiation
PubMed: 37747885
DOI: 10.1128/msystems.00425-23 -
The Science of the Total Environment Jan 2024Predatory myxobacteria are important soil micropredators with the potential to regulate soil microbial community structure and ecosystem function. However, the...
Predatory myxobacteria are important soil micropredators with the potential to regulate soil microbial community structure and ecosystem function. However, the biogeographic distribution patterns, assembly processes, and potential nutrient cycling functions of myxobacteria communities in typical agricultural soils in China are still poorly understood. High-throughput sequencing, phylogenetic zero modeling, and the multi-nutrient cycling index were used to assess the biogeographic distribution, assembly processes, and soil ecosystem functions of predation myxobacteria communities in typical agricultural soils of six long-term fertilization ecological experimental stations. The results demonstrated a hump-shaped distribution of myxobacteria α-diversity along the latitudinal gradient and significant differences in myxobacteria β-diversity in typical agricultural soils (P < 0.05). Bacterial richness, soil organic carbon, and pH were the most important predictors of myxobacteria α-diversity, whereas geographic factors and soil pH were the most significant ecological predictors of myxobacteria β-diversity. Myxobacteria community assembly is dominated by deterministic processes, especially homogeneous selection, primarily driven by soil pH and bacterial richness. In addition, we revealed the ecological significance of myxobacteria communities in typical agricultural soil microbial networks and the potential link between myxobacteria communities and soil nutrient cycling. These findings enhance our understanding of the biogeographic distribution, community assembly, ecological predictors, and relationships with soil nutrient cycling of myxobacteria communities in typical agricultural soils, paving the way for a more predictive understanding of the effect of predatory myxobacteria communities on soil ecosystem function, which is essential for the development of sustainable agriculture.
Topics: Soil; Myxococcales; Phylogeny; Carbon; Soil Microbiology; Agriculture; Bacteria; Microbiota; China
PubMed: 37741390
DOI: 10.1016/j.scitotenv.2023.167255 -
Nature Communications Sep 2023Public metabolites such as vitamins play critical roles in maintaining the ecological functions of microbial community. However, the biochemical and physiological bases...
Public metabolites such as vitamins play critical roles in maintaining the ecological functions of microbial community. However, the biochemical and physiological bases for fine-tuning of public metabolites in the microbiome remain poorly understood. Here, we examine the interactions between myxobacteria and Phytophthora sojae, an oomycete pathogen of soybean. We find that host plant and soil microbes complement P. sojae's auxotrophy for thiamine. Whereas, myxobacteria inhibits Phytophthora growth by a thiaminase I CcThi1 secreted into extracellular environment via outer membrane vesicles (OMVs). CcThi1 scavenges the required thiamine and thus arrests the thiamine sharing behavior of P. sojae from the supplier, which interferes with amino acid metabolism and expression of pathogenic effectors, probably leading to impairment of P. sojae growth and pathogenicity. Moreover, myxobacteria and CcThi1 are highly effective in regulating the thiamine levels in soil, which is correlated with the incidence of soybean Phytophthora root rot. Our findings unravel a novel ecological tactic employed by myxobacteria to maintain the interspecific equilibrium in soil microbial community.
Topics: Glycine max; Thiamine; Phytophthora; Myxococcales; Rhizosphere; Blister
PubMed: 37704617
DOI: 10.1038/s41467-023-41247-0 -
ACS Chemical Biology Oct 2023Myxobacteria exhibit a substantial capacity to produce bioactive natural products. The biosynthetic potential of ribosomally synthesized and post-translationally...
Myxobacteria exhibit a substantial capacity to produce bioactive natural products. The biosynthetic potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) from myxobacteria remains largely underexplored. In our study, we identified a novel lanthipeptide-like biosynthetic pathway, from sp. MCy9171, which was reconstituted in and proteolysis. Structural elucidation demonstrated that a series of dehydroamino acids were installed by an orphan McyB dehydratase onto the five McyA core peptides, named myxopeptins. Interestingly, compared with the canonical biosynthetic machinery of class I lanthipeptides, neither Cys residues existed in the diverse core regions, nor any LanC cyclase homologue was encoded in the pathway. Thus, we propose myxopeptins as members of a new subclass of RiPPs, named lanthipeptide-derived linear dehydroamino acid-containing peptides (LDPs), which contain dehydrated amino acids as the class-defining post-translational modifications. Furthermore, sequence similarity network (SSN) analysis revealed the wide distribution of the biosynthetic potential of LDPs in various microbial phyla, implying a co-evolutionary scenario between the precursor peptide and class I lanthipeptide biosynthetic enzymes.
Topics: Myxococcus; Escherichia coli; Peptides; Protein Processing, Post-Translational
PubMed: 37703191
DOI: 10.1021/acschembio.3c00265 -
Nature Communications Sep 2023Many species, such as fish schools or bird flocks, rely on collective motion to forage, prey, or escape predators. Likewise, Myxococcus xanthus forages and moves...
Many species, such as fish schools or bird flocks, rely on collective motion to forage, prey, or escape predators. Likewise, Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial species. These activities require two distinct motility machines enabling adventurous (A) and social (S) gliding, however when and how these mechanisms are used has remained elusive. Here, we address this long-standing question by applying multiscale semantic cell tracking during predation. We show that: (1) foragers and swarms can comprise A- and S-motile cells, with single cells exchanging frequently between these groups; (2) A-motility is critical to ensure the directional movement of both foragers and swarms; (3) the combined action of A- and S-motile cells within swarms leads to increased predation efficiencies. These results challenge the notion that A- and S-motilities are exclusive to foragers and swarms, and show that these machines act synergistically to enhance predation efficiency.
Topics: Animals; Predatory Behavior; Cell Tracking; Cooperative Behavior; Motion; Myxococcus xanthus
PubMed: 37696789
DOI: 10.1038/s41467-023-41193-x -
Journal of Bacteriology Sep 2023The regulation of biofilm and motile states as alternate bacterial lifestyles has been studied extensively in flagellated bacteria, where the second messenger...
The regulation of biofilm and motile states as alternate bacterial lifestyles has been studied extensively in flagellated bacteria, where the second messenger cyclic-di-GMP (cdG) plays a crucial role. However, much less is known about the mechanisms of such regulation in motile bacteria without flagella. The bacterial type IV pilus (T4P) serves as a motility apparatus that enables to move on solid surfaces. PilB, the T4P assembly ATPase, is, therefore, required for T4P-dependent motility in . Interestingly, T4P is also involved in the regulation of exopolysaccharide as the biofilm matrix material in this bacterium. A newly discovered cdG-binding domain, MshE, is conserved in the N-terminus of PilB (PilB) in and other bacteria. This suggests that cdG may bind to PilB to control the respective outputs that regulate biofilm development and T4P-powered motility. In this study, we aimed to validate PilB as a cdG effector protein. We performed a systematic mutational analysis of its cdG-binding domain to investigate its relationship with motility, piliation, and biofilm formation. Excluding those resulting in low levels of PilB protein, all other substitution mutations in PilB resulted in mutants with distinct and differential phenotypes in piliation and biofilm levels in . This suggests that the PilB domain plays dual roles in modulating motility and biofilm levels, and these two functions of PilB can be dependent on and independent of each other in . IMPORTANCE The regulation of motility and biofilm by cyclic-di-GMP in flagellated bacteria has been extensively investigated. However, our knowledge regarding this regulation in motile bacteria without flagella remains limited. Here, we aimed to address this gap by investigating a non-flagellated bacterium with motility powered by bacterial type-IV pilus (T4P). Previous studies hinted at the possibility of PilB, the T4P assembly ATPase, serving as a cyclic-di-GMP effector involved in regulating both motility and biofilm. Our findings strongly support the hypothesis that PilB directly interacts with cyclic-di-GMP to act as a potential switch to promote biofilm formation or T4P-dependent motility. These results shed light on the bifurcation of PilB functions and its pivotal role in coordinating biofilm formation and T4P-mediated motility.
Topics: Myxococcus xanthus; Cyclic GMP; Adenosine Triphosphatases; Biofilms
PubMed: 37695853
DOI: 10.1128/jb.00221-23