npj Biofilms and Microbiomes最新文献

Osteomyelitis, an infection of bone, is traditionally treated with long-term, systemic, high-dose antibiotics, which can lead to kidney and liver damage and accelerate the development of antibiotic resistance. Localized delivery may mitigate these risks by delivering antimicrobial(s) directly to the site of infection. Herein, innately antimicrobial chitosan hydrogel (CH) containing polylactic acid (PLA) microparticles, each loaded with fosfomycin antibiotic, was used to combat a biofilm-forming strain of Staphylococcus aureus. This dual CH + PLA biomaterial treatment mitigated S. aureus in planktonic and biofilm form in vitro, and in a clinically relevant, implant-associated rat model of chronic osteomyelitis. Notably, only the CH + PLA biomaterial treatment led to a reduction in bone defect area, plasma haptoglobin level, and bacterial burden in bone and soft tissue, compared to hydrogel only. Local treatment of osteomyelitis with the chitosan+microparticle vehicle loaded with fosfomycin mitigated S. aureus pathogenesis and may serve as an effective alternative to systemic antibiotics.

Using multi-omics tools, we discovered new antimicrobial peptides (AMPs) and examined AMP-microbial interactions in three Appalachian salamander species (Plethodon cinereus, Eurycea bislineata and Notophthalmus viridescens). We conducted skin transcriptomics (n = 13) and proteomics (n = 91) to identify 200+ candidate AMPs. With candidate AMPs, we identified correlations with skin microbiomes and synthesized 20 peptides to challenge against pathogens of amphibians (Batrachochytrium dendrobatidis: Bd) and humans (ESKAPEE). Using transcriptomics, candidate AMPs were detected in all individuals with Cathelidicins being most common. Using proteomics, AMPs were found in 34% of individuals (31/91)-predominately E. bislineata-with Kinin-like peptides being most common. Candidate AMP composition generally predicted skin bacterial composition, suggesting that AMPs influence host-microbial symbioses. Crude and synthesized peptides showed limited activity against Bd. Two synthesized Cathelicidins (Pcin-CATH3 and Pcin-CATH5) inhibited human pathogens, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli. Our findings inform the potential usage of AMPs in conservation and translational applications.

Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.

Biofilm formation by Klebsiella pneumoniae is mediated by the type 3 fimbriae Mrk, and regulated by MrkH and 3',5'-cyclic diguanylic acid (c-di-GMP). We sought to identify specific chemical inhibitors of K. pneumoniae biofilm formation that reduced the activity of MrkH. A compound N-(3-cyano-5,6,7,8-tetrahydro-4H-cyclohepta[b]thien-2-yl)-2-methoxybenzamide, JT71, reduced K. pneumoniae mrkA promoter activity and biofilm formation by 50% without affecting cell viability. Western blot analysis, hemagglutination assays, electron microscopy and qPCR showed that JT71 reduced type 3 fimbriae production, and transcription of mrkA and mrkH. JT71 demonstrated activity against other clinical and multi-drug resistant K. pneumoniae isolates, and a type 3 fimbriate-positive Citrobacter koseri strain. In silico molecule docking was used to illustrate that JT71 could bind directly to the MrkH protein and block its activity. JT71 possesses promising drug-likeness properties and is non-toxic to mammalian cells. Chemical inhibition of transcriptional regulators that control fimbriae expression can inhibit bacterial biofilm formation.

Bacteria commonly protect themselves from a variety of threats by forming biofilms, which are communities of bacteria that are tightly packed together within an extracellular matrix. Biofilm formation has generally been thought to protect bacteria from phage infection. The opportunistic pathogen Pseudomonas aeruginosa produces biofilm matrices that can contain three distinct exopolysaccharides that contribute to the difficulty in treating infected patients. Here, we demonstrate that two diverse P. aeruginosa phages have evolved to exploit this biofilm matrix to access the bacterial cells by both binding to and degrading a major biofilm exopolysaccharide, Psl. We examined the effect of these phages on biofilms in different in vitro biofilm models and found that both phages prevent bacterial surface attachment, but only one of the two phages can disrupt a mature biofilm under flow. The phages also rapidly lead to the emergence of bacterial strains that produce reduced amounts of Psl and are unable to adhere to surfaces. These phages may be useful therapeutically by driving bacteria away from producing biofilms and shifting P. aeruginosa cells into the more treatable planktonic growth state.

Carcass microbial decomposition plays a vital role in global elemental cycling. However, bacterial and fungal absolute abundance dynamics, as well as their contributions to carcass decomposition, remain unclear. Here, the questions were investigated through quantitative microbiome profiling (QMP) and metabolomics. Within the first 14 days postmortem, microbial copies in grave soil and tissue increased by several orders of magnitude. Comparison of QMP with relative microbiome profiling (RMP) revealed strikingly different, even opposing successional trends for major phyla. Bacteria drove more metabolite variation than fungi in the decomposition. Co-occurrence networks revealed that key bacterial and fungal decomposers formed two distinct modules that were highly interconnected and significantly associated with carcass-derived metabolites, suggesting a synergistic relationship in the breakdown of organic matter. Notably, using QMP did not substantially enhance the accuracy of postmortem interval estimation. Collectively, our findings provide critical insights into microbial ecological dynamics during carcass decomposition.

Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.

Antimicrobial resistance is a major global health threat, potentially causing 8.22 million deaths annually by 2050. Polymicrobial biofilms significantly contribute to this crisis, leading to treatment failure, especially in chronic airway infections caused by Staphylococcus aureus and Pseudomonas aeruginosa, common in ventilator-associated pneumonia and cystic fibrosis. To address this, we engineered an attenuated Mycoplasma pneumoniae strain, CV8_HAD, to secrete biofilm-disrupting enzymes (PelAh, PslGh, A1-II' and Dispersin B). CV8_HAD showed strong in vitro activity against single and mixed-species biofilms of S. aureus and P. aeruginosa, and demonstrated in vivo efficacy against S. aureus biofilms in mice and mixed infections in Galleria mellonella larvae. This study establishes engineered M. pneumoniae as a promising therapeutic strategy for tackling microbial biofilms and highlights the potential of G. mellonella larvae models as an alternative to mouse models in advancing research on biofilm-targeting interventions.

Dental plaque is a complex oral biofilm responsible for periodontal diseases. Bacterial biofilms are often regulated by Quorum Sensing (QS) mediated by N-acyl homoserine lactones (AHLs). While their presence and roles in oral microbiota have been debated, emerging evidence suggests AHLs influence oral biofilm development. AHLs are detectable in a microbial community derived from human dental plaque cultured under 5% CO₂ but not under anaerobic conditions. Manipulating QS in this community via AHL lactonases enriched commensals and pioneer colonizers under 5% CO₂, whereas in anaerobic conditions exogenous AHLs promoted late colonizers. QS disruption reduced biofilm formation, enhanced sucrose fermentation to lactate, and altered metabolic profiles of the community depending on the lactonase substrate specificity. Our findings highlight the importance of AHL-mediated QS in oral biofilm development and suggest its differential roles under aerobic versus anaerobic conditions. Targeting QS may offer a novel strategy for managing oral biofilms and preventing periodontal disease.

The female microbiome is emerging as a key regulator of gynecological and reproductive health. This review summarizes how local and gut microbes affect gynecological outcomes, fertility, and pregnancy through metabolic, immune, and hormonal pathways. We highlight underlying mechanisms and intervention strategies, emphasizing the restoration of microbial homeostasis as a promising avenue for advancing understanding, prevention, and management of women's physiological and reproductive health conditions.