Search Results (82)

As the primary biological risk threatening safe dairy production, bovine mastitis control highly relies on environmental disinfection measures. However, the mechanisms by which chemical disinfectants influence host–environment microbial interactions remain unclear. This study systematically investigated the disinfection efficacy and regulatory effects on microbial community composition and diversity of glutaraldehyde-benzalkonium chloride (BAC) and glutaraldehyde-didecyl dimethyl ammonium bromide (DAB) at recommended concentrations (2–5%), using 80 environmental samples from intensive dairy farms in Xinjiang, China. Combining 16S rDNA sequencing with culturomics, the results showed that BAC achieved a disinfection rate of 99.33%, higher than DAB’s 97.87%, and reduced the environment–gut microbiota similarity index by 23.7% via a cationic bacteriostatic film effect. Microbiome analysis revealed that BAC selectively suppressed Fusobacteriota abundance (15.67% reduction) and promoted Bifidobacterium proliferation (7.42% increase), enhancing intestinal mucosal barrier function through butyrate metabolism. In contrast, DAB induced Actinobacteria enrichment in the environment (44.71%), inhibiting pathogen colonization via bioantagonism. BAC’s long-acting bacteriostatic properties significantly reduced disinfection costs and mastitis incidence. This study first elucidated the mechanism by which quaternary ammonium compound (QAC) disinfectants regulate host health through “environment-gut” microbial interactions, providing a critical theoretical basis for developing precision disinfection protocols integrating “cost reduction-efficiency enhancement-risk mitigation.” Full article

Mink (Neogale vison) is a commercially farmed animal of global importance. However, disease outbreaks during farming not only cause significant economic losses but also substantially increase the risk of zoonotic infections. The identification and characterization of pathogenic bacteria remain a major bottleneck restricting the development of healthy and sustainable mink farming. In this study, an LB medium was used to isolate a pale-white, rod-shaped, Gram-negative bacterial strain, Qf-1, from minks with pneumonia. Based on morphological characteristics, biochemical properties, 16S rRNA gene sequencing, and average nucleotide identity (ANI) analysis, strain Qf-1 was identified as Huaxiibacter chinensis Qf-1. Under laboratory conditions, H. chinensis Qf-1 induced typical pneumonia symptoms in Kunming mice. Furthermore, whole-genome sequencing of H. chinensis Qf-1 revealed its genome to be 4.77 Mb and to contain a single chromosome and one plasmid. The main virulence genes of H. chinensis Qf-1 were primarily associated with flgB, flgC, flgG, aceA, hemL, tssC1, csgD, hofB, ppdD, hcpA, and vgrGA, functioning in motility, biofilm formation, colonization ability, and secretion systems. Our findings contribute to a better understanding of their pathogenic mechanisms, thereby laying a theoretical foundation for further investigation into the complex interactions between gut microbiota and the host. Full article

The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing follicles and used for microbiota propagation. Bacterial pellets underwent 16S rRNA gene sequencing and targeted culturomics, whereas cell-free supernatants were used as supplements for the in vitro maturation (IVM) of slaughtered PLOs. For the first time, bacteria presence in adult sheep FF was detected, with the first report of Streptococcus infantarius subsp. infantarius (as a species) and Burkholderia cepacia (as a genus and species) in either animal or human FF. The short- and long-term effects of bacterial metabolites on PLO maturation and embryonic development were demonstrated. As short-term effects, the addition of FF microbiota metabolites did not affect the oocyte nuclear maturation and mitochondria distribution pattern, except in one of the examined supernatants, which reduced all quantitative bioenergetic/oxidative parameters. As long-term effects, one of them reduced the total cleavage rate after in vitro embryo culture (IVC). In conclusion, microbiota/bacteria are present in adult sheep FF and may influence reproductive outcomes in vitro. Future studies may reveal the beneficial in vitro effects using the microbiome from preovulatory follicles. Full article

Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems. Full article

The human microbiome plays a critical role in health and disease, with recent innovations in microbiome research offering groundbreaking insights that could reshape the future of healthcare. This study explored emerging methodologies, such as long-read sequencing, culturomics, synthetic biology, machine learning, and AI-driven diagnostics, that are transforming the field of microbiome–host interactions. Unlike traditional broad-spectrum approaches, these tools enable precise interventions, such as detecting foodborne pathogens and remediating polluted soils for safer agriculture. This work highlights the integration of interdisciplinary approaches and non-animal models, such as 3D cultures and organ-on-a-chip technologies, which address the limitations of current research and present ethical, scalable alternatives for microbiome studies. Focusing on food safety and environmental health, we examine how microbial variability impacts pathogen control in food chains and ecosystem resilience, integrating socioeconomic and environmental factors. The study also emphasizes the need to expand beyond bacterial-focused microbiome research, advocating for the inclusion of fungi, viruses, and helminths to deepen our understanding of therapeutic microbial consortia. The combination of high-throughput sequencing, biosensors, bioinformatics, and machine learning drives precision strategies, such as reducing food spoilage and enhancing soil fertility, paving the way for sustainable food systems and environmental management. Hence, this work offers a comprehensive framework for advancing microbiome interventions, providing valuable insights for researchers and professionals navigating this rapidly evolving field. Full article

The Anthropocene is a concept that highlights the profound changes humans have made to nearly every aspect of the Earth. It serves as a compelling narrative that challenges us to examine public perceptions and interests regarding human–nature interactions in an integrated way. These interactions are widespread but can vary significantly over time, across cultures and under different economic conditions, making them difficult to monitor effectively on a large scale. Recent advancements in digital technology, such as the ability to track online searches through tools, like Google Trends-Glimpse, and the near real-time monitoring of news broadcasts via the GDELT Project, present new opportunities. These tools can analyze data in multiple languages around the world, encouraging innovative approaches to integrate the diverse and complex information generated within this multi-language, multi-concept, and varied time-scale environment of human activity and beliefs. We propose a transformed version of Markowitz’s multi-asset optimization theory that encompasses over 5.5 billion people, several languages, and concepts since 2004. This approach is a functional ensemble where ecology and economics intersect, at least mechanistically. Our findings indicate that while there is a general increase in people’s interest in Anthropocene-related issues, significant differences exist across cultures. We also identify several sources of data noise and evidence that interfere with the overall methodology. Addressing these issues in future research will help to extend the validity of our approach, especially if it increases interest in conservation culturomics. Full article

Background: European wild rabbits (Oryctolagus cuniculus) are closely connected to the natural environment and might be a potential source of pathogenic bacteria and/or antimicrobial-resistant bacteria. The objective was to identify the bacterial community (species and genera) that colonizes the nasal cavities of European wild rabbits as well as to study the antimicrobial resistance (AMR) phenotypes of bacteria of public health interest. Methods: A total of 147 nasal swabs individually collected from wild rabbits in Spain and Portugal (between 2022 and 2024) were studied. Samples were inoculated in different culture media, and isolates were identified by MALDI-TOF. The AMR phenotypes of staphylococci, mammaliicocci, enterococci and Enterobacterales were evaluated by the disk-diffusion method. Results: Overall, 557 non-repetitive isolates were obtained (1 isolate per species and AMR phenotype of each animal). A wide diversity of genera (n = 40) and species (n = 90) was found. Staphylococcus (21.2%), Mammaliicoccus (11.7%), Enterococcus (23.3%), Enterobacter (9.2%), Citrobacter (4.5%) and Escherichia (5.9%) were the most detected genera. Most animals presented more than one genera (78.9%), and in 15.7% of them, at least five genera were identified. Susceptibility to all antimicrobials tested was found in 37.2%, 38.5% and 51.6% of staphylococci/mammaliicocci, enterococci and Escherichia coli isolates; moreover, multidrug resistance was detected in 10.4%, 14.6% and 9.6% of these groups of bacteria. Moreover, important species of pathogenic bacteria were found, such as Yersinia enterolocolitica (0.5%) and Bordetella bronchiseptica (0.2%), among others. Conclusions: A high bacterial diversity was detected in the nasal cavities of European wild rabbits from the Iberian Peninsula, including pathogenic species and/or resistant strains of public health interest. Full article

The composition of the human microbiome is a critical health indicator, and culture-independent methodologies have substantially advanced our understanding of human-associated microorganisms. However, precise identification and characterization of microbial strains require culture-based techniques. Recently, the resurgence of culturomics, combined with high-throughput sequencing technology, has reduced the high labor demand of pure culture methods, facilitating a more efficient and comprehensive acquisition of culturable microbial strains. This study employed an integrated approach combining culturomic and high-throughput sequencing to identify culturable microorganisms on the human scalp and in human saliva and feces. Several Staphylococcus strains were identified from the scalp, whereas anaerobic microorganisms were dominant in the saliva and fecal samples. Additionally, the study highlighted the beneficial effects of transportation conditions (liquid nitrogen treatment, dry ice transport, and dimethyl sulfoxide [DMSO] buffer) in preserving culturable microorganisms. A robust methodology was developed for the large-scale acquisition of culturable microorganisms with optimized transport conditions that enhance the potential for isolating a greater diversity of culturable strains. Full article

Gampsocleis gratiosa Brunner von Wattenwyl, 1862, is a type of omnivorous chirping insect with a long history of artificial breeding. It has high economic value and is also an excellent orthopteran model organism. In this study, 12 types of culture media combined with 16S rRNA sequencing were employed to isolate 838 bacterial strains from the gut of G. gratiosa. After sequence comparison, a total of 98 species of bacteria were identified, belonging to 3 phyla, 5 classes, 11 orders, 20 families, and 45 genera. Firmicutes and Proteobacteria accounted for the majority (92.86%). At the order level, Enterobacteriaceae, Bacillales, and Lactobacillales predominated (79.59%). At the genus level, Klebsiella (11.22%) and Enterococcus (7.14%) predominated. This study also enumerated the strain morphological, physiological and biochemical properties of 98 species of bacteria, including colony morphology, Gram staining, bacterial motility test, temperature gradient growth, pH gradient growth, citrate utilization test, temperature oxidase test, contact enzyme test, methyl red test, V-P test, indole test, gelatin liquefaction test, nitrate reduction test, hydrogen sulfide test, starch hydrolysis test, cellulose decomposition test, esterase (corn oil) test and antibiotic susceptibility testing. Additionally, 16 antibiotics were utilized to test the bacterial susceptibility of the strains. This study explored the types and community structure of some culturable microorganisms in the intestinal tract of G. gratiosa and recorded their physiological characteristics. These data reflect the physiological functions of the intestinal microorganisms of G. gratiosa and provide support for subsequent research on the interaction mechanism between microorganisms and their hosts. Full article

Dietary exposure to the plasticiser bisphenol A (BPA), an obesogenic and endocrine disruptor from plastic and epoxy resin industries, remains prevalent despite regulatory restriction and food safety efforts. BPA can be accumulated in humans and animals, potentially exerting differential health effects based on individual metabolic capacity. This pilot study examines the impact of direct ex vivo BPA exposure on the gut microbiota of obese and normal-weight children, using 16S rRNA amplicon sequencing and anaerobic culturing combined methods. Results showed that direct xenobiotic exposure induced modifications in microbial taxa relative abundance, community structure, and diversity. Specifically, BPA reduced the abundance of bacteria belonging to the phylum Bacteroidota, while taxa from the phylum Actinomycetota were promoted. Consistently, Bacteroides species were classified as sensitive to BPA, whereas bacteria belonging to the class Clostridia were identified as resistant to BPA in our culturomics analysis. Some of the altered bacterial abundance patterns were common for both the BPA-exposed groups and the obese non-exposed group in our pilot study. These findings were also corroborated in a larger cohort of children. Future research will be essential to evaluate these microbial taxa as potential biomarkers for biomonitoring the effect of BPA and its role as an obesogenic substance in children. Full article

Background/Objectives: Several independent studies have associated prostate cancer (PCa) with specific groups of bacteria, most of them reporting the presence of anaerobic or microaerophilic species such as Cutibacterium acnes (C. acnes). Such findings suggest a prostate cancer-related bacterial dysbiosis, in a manner similar to the association between Helicobacter pylori infection and gastric cancer. In an earlier exploratory study looking for such dysbiosis events, using a culturomics approach, we discovered that the presence of obligate anaerobes (OAs) along with C. acnes was associated with increased prostate-specific antigen (PSA) levels in 39 participants. Methods: Building on this, in this study, we analyzed 89 post-rectal examination urine samples, from men with prostate cancer attending the PROVENT trial, using 16S rDNA sequencing. Our investigation focused on the impact of six previously identified OA genera (Finegoldia, Fusobacterium, Prevotella, Peptoniphilus_A, Peptostreptococcus, and Veillonella_A) on PSA levels. However, an additional data-driven approach was followed to uncover more taxa linked to increased PSA. Results: Our analysis revealed a statistically significant association between Peptostreptococcus and elevated PSA levels. Additionally, there were potential interactions between Prevotella and Fusobacterium. Interestingly, we also found that an aerobe, Ochrobactrum_A,was significantly linked to higher PSA levels. Conclusions: These findings suggest that OA-related dysbiosis may contribute to elevated PSA levels through prostate cell damage even before prostate cancer develops, possibly playing a role in chronic inflammation and the hypervascular changes seen in precancerous lesions. Future clinical trials with larger cohorts are needed to further evaluate the role of OA in prostate cancer development and progression. Full article

Gut microbiota (GM), together with its metabolites (such as SCFA, tryptophan, dopamine, GABA, etc.), plays an important role in the functioning of the central nervous system. Various neurological and psychiatric disorders are associated with changes in the composition of GM and their metabolites, which puts them in the foreground as a potential adjuvant therapy. However, the molecular mechanisms behind this relationship are not clear enough. Therefore, before considering beneficial microbes and/or their metabolites as potential therapeutics for brain disorders, the mechanisms underlying microbiota–host interactions must be identified and characterized in detail. In this review, we summarize the current knowledge of GM alterations observed in prevalent neurological and psychiatric disorders, multiple sclerosis, major depressive disorder, Alzheimer’s disease, and autism spectrum disorders, together with experimental evidence of their potential to improve patients’ quality of life. We further discuss the main obstacles in the study of GM–host interactions and describe the state-of-the-art solution and trends in this field, namely “culturomics” which enables the culture and identification of novel bacteria that inhabit the human gut, and models of the gut and blood–brain barrier as well as the gut–brain axis based on induced pluripotent stem cells (iPSCs) and iPSC derivatives, thus pursuing a personalized medicine agenda for neuropsychiatric disorders. Full article

The exploration of microbial genetic resources for the production of fFen-flavor Baijiu has not only enriched the microbial library for baijiu production but has also laid the foundation for process improvement and strain optimization in baijiu brewing. In this study, a total of 177 fungal isolates were screened, including Saccharomyces cerevisiae, non-Saccharomyces cerevisiae, molds, and some pathogenic bacteria. Among them, Saccharomyces cerevisiae was the most abundant with 119 isolates, playing a major role in the fermentation of baijiu production. A total of 148 bacterial isolates were obtained from the fermentation mash samples, showing greater diversity compared to fungi. Bacillus species were the most abundant, with 94 isolates. Bacillus licheniformis, in particular, can produce a rich enzymatic system and flavor precursors, making it an important contributor to the sensory quality of baijiu. Lactic acid bacteria were the second most abundant, with 16 isolates. Additionally, five pathogenic fungal species were identified, including Candida pelliculosa, Candida lusitaniae, Fusarium oxysporum, Fusarium solani and Talaromyces marneffei. Six pathogenic bacterial species were also isolated, namely Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus xylosus, Moraxella osloensis, Actinomyces meyeri and Stenotrophomonas maltophilia. Finally, two strains of high acetate ethyl ester-producing yeast and lactate-degrading bacteria with good tolerance to temperature, pH, and ethanol concentration were identified as Saccharomyces cerevisiae and Bacillus licheniformis, respectively. Full article

The discovery of natural products has been pivotal in drug development, providing a vast reservoir of bioactive compounds from various biological sources. This narrative review addresses a critical research gap: the largely underexplored role of gut microbiota in the mediation and biotransformation of medicinal herb-derived natural products for therapeutic use. By examining the interplay between gut microbiota and natural products, this review highlights the potential of microbiota-mediated biotransformation to unveil novel therapeutic agents. It delves into the mechanisms by which gut microbes modify and enhance the efficacy of natural products, with a focus on herbal medicines from Ayurveda and traditional Chinese medicine, known for their applications in treating metabolic and inflammatory diseases. The review also discusses recent advances in microbiota-derived natural product research, including innovative methodologies such as culturomics, metagenomics, and metabolomics. By exploring the intricate interactions between gut microorganisms and their substrates, this review uncovers new strategies for leveraging gut microbiota-mediated processes in the development of groundbreaking therapeutics. Full article

Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species’ identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles. Full article