Frontiers in microbiomes最新文献

Introduction: The cutaneous microbiome plays an essential role in guarding against invasive pathogens and maintaining healthy skin homeostasis. Several studies have demonstrated the importance of a healthy skin microbiome through its alteration in several diseases. Differing skin characteristics across the body (temperature, pH, humidity) create distinct ecological niches inhabited by diverse microbial communities. The study of cutaneous microbiota is further complicated by numerous variables at all stages of investigation, including study design, skin sampling method, sample storage, sample processing, sequencing, and data analysis. Utilisation of standardised approaches is critical for reproducibility and comparison between skin microbiome studies. However, there is a notable lack of standardisation of sampling methodologies in the literature. Studies have employed differing sampling strategies and conditions which may affect microbiota characterisation.

Methods: Antecubital fossa was sampled from sixteen individuals using sterile dry cotton swabs or eSwabs. Sterile phosphate buffered saline, or 0.9% sterile saline were used as moistening solutions. Samples were then either stored at room temperature for 30 minutes or stored at -80°C for at least 24 hours before processing. Cutaneous microbiome was identified using 16S sequencing.

Results: Comparative analysis determined whether the type of swab (cotton/eSwab), moistening solution (saline solution/phosphate buffered saline), duration of swabbing (30 sec/1 min), and sample storage temperature (room temperature/-80°C) affect sampling and identification of skin microbial communities. Comparison of the total DNA yield extracted using different conditions showed that while moistening solution, duration of swabbing, and storage conditions did not affect the total DNA amount, using eSwabs yielded higher biomass.

Discussion: Sampling approaches are critical for the success of sequencing. The conditions investigated in this study did not influence microbiome profiling allowing consistent sampling of the microbiota. However, data clustering was affected more by individual subject than by the conditions investigated, suggesting the importance of recognizing inter-individual variability as an important factor in real-life skin microbiome studies.

Introduction: Humans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.

Methods: In this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.

Results: VOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC-acetoin (3-hydroxy, 2-butanone)-was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.

Alfalfa forms and rumen degradable starch (RDS) levels in diets can profoundly affect growth performance and rumen fermentation patterns, this influence may result in variations in rumen microbiota. However, the effects of RDS levels on methanogenic and fungal communities in alfalfa hay (AH) or alfalfa silage (AS) diets, and the interaction between methanogens and fungi with growth performance and rumen fermentation patterns, remain unknown. In this study, a 2 × 2 factorial design resulted in four diets: two alfalfa forms (AH and AS) and two RDS levels (LR: 14.85% DM RDS; and HR: 20.21% DM RDS). We used 32 female Suffolk sheep for the experiment. On day 75 (including a 15-day transition period and a 60-day trial period), rumen content was collected after slaughter to examine the ruminal methanogens and fungi. The AHHR diet reduced the methanogen Chao 1 index compared to the AS diets (P < 0.05), and the Shannon index was lower than in the ASLR diet (P < 0.05). The fungi Chao 1 index was higher in the AH diets than in the ASHR diet (P < 0.05), and the fungi Shannon index was higher in the LR diets than in the HR diets (P < 0.05). The relative abundance of Aspergillus in the AHLR diet was significantly higher than in the AS diets (P < 0.01), and the relative abundance of Occultifur and Meyerozyma were decreased in the AH diets than in the AS diets (P < 0.05). The LEfSe analysis showed that Methanobrevibacter_sp_YE315 and Methanobrevibacter_sp_AbM4 were enriched in the ASLR diet, while Methanobrevibacter_millerae was enriched in the ASHR diet. For the fungal biomarkers, the AHLR diet included Aspergillus, Metschnikowia, and unclassified_f:Stachybotryaceae; the AHHR diet included stachybotrys, Stemphylium, and Cystobasidium; the ASLR diet included unclassified_k:Fungi, Trichothecium, and Psathyrella; and the ASHR diet included Alfaria. The correlation analysis results showed the relative abundance of Methanobrevibacter, Methanoculleus, Penicillium, Cladosporium, and Exophiala and the concentrations of isobutyrate and isovalerate, which may provide deeper insights into the previously observed differences.

Introduction: The nutritional level of the diet plays a crucial role in maintaining the balance of the yak rumen microbiota. To explore the relationship between dietary nutritional levels, the rumen microbiota, and muscle metabolites, we examined the characteristics of the yak rumen microbiota and muscle metabolome under different dietary nutritional levels.

Methods: Randomly divide 24 yaks with similar body weights, [235.96 ± 12.46 kg], into three groups. These groups were subjected to three nutritional feeding levels: ad libitum feeding (AL), 70% of ad libitum intake (IR70), and 40% of ad libitum intake (IR40). When the yaks in the AL group gained 70 kg in body weight, they were slaughtered.

Results: The results indicated that the ad libitum feeding group (AL) demonstrated superior edible meat quality in terms of Chroma L*, Chroma a*, and shear force, compared to the 70% intake group (IR70) and the 40% intake group (IR40). At the phylum level, the abundance of Patescibacteria was notably greater in the IR40 group compared to both the AL group and the IR70 group. At the genus level, the relative abundance of Succinimonas was higher in the AL group than in both the IR70 and IR40 groups. Untargeted metabolomics analysis revealed that the levels of metabolites such as 5-Methylcytosine, Cytosine, and Thymine were upregulated in the longissimus dorsi muscle of the AL group, which contributed to the enhancement of meat flavor. Furthermore, Spearman's correlation analysis revealed a notable relationship between the rumen microbiota and both meat quality and metabolite levels. pH45min is positively correlated with trans-Cinnamic acid. Methanobrevibacter exhibited a positive correlation with the concentration of 4-(Diethylamino)benzaldehyde, while Candidatus_Saccharimonas showed a positive correlation with the concentration of phenylacetylglycine.

Discussion: This study provides scientific evidence for understanding the impact of different nutritional feeding conditions on yak meat quality, rumen microbiota, and related muscle metabolomic pathways. It also reveals the potential impact of these factors on meat flavor. These findings offer important reference information for optimizing yak husbandry management, improving the formation of beef flavor compounds, and understanding their regulatory mechanisms.

Diabetes mellitus is a prevalent chronic non-communicable disease, and recent studies have explored the link between gut microbiota and its development. Despite some evidence suggesting an association, the influence of gut microbiota on type 2 diabetes (T2D) remains unclear. A systematic search of PubMed (January 2016- December 2023) using the keywords "16S" and "diabetes" or "DM2" or "T2DM" or "T2D" and "gut microbiota" and "diabetes" or "DM2" or "T2DM" or "T2D". The studies included compared gut microbiome diversity between diabetic and non-diabetic adults using 16S rRNA sequencing, excluding children, interventions, and type 1 diabetes. Alpha diversity indices and bacterial mean abundance were analyzed, with statistical assessments using a random-effects model and I² for heterogeneity. Thirteen studies met the criteria, with the Shannon index being the most commonly used measure. Results showed significant heterogeneity (I² > 75%) and no notable differences between diabetic and non-diabetic groups. Other indices, such as Chao1 and phylogenetic whole tree, similarly showed no consistent differences. Taxonomic analysis also failed to find phyla consistently correlated with T2D, with variability across studies. The relationship between gut microbiota and diabetes remains uncertain due to technical and biological factors that are often overlooked. The inconsistencies across studies highlight the low reproducibility common in microbiota research.

Postbiotics, which are bioactive compounds derived from the metabolic processes of probiotics, are gaining recognition as a promising alternative for managing chronic diseases without the need for live microorganisms, positioning them as a valuable strategy in biotherapeutics that offers both curative and preventive techniques in modern medicine. This paper provides a comprehensive review of the potential health benefits of postbiotics, particularly concerning noncommunicable diseases like diabetes, cancer, obesity and cardiovascular conditions, which present significant global health challenges. We explore the various mechanisms by which postbiotics exert their beneficial effects, including immune modulation to enhance the body's immune response and reduce inflammation, as well as improving gut barrier function to maintain gut integrity and prevent increased intestinal permeability. Additionally, the antioxidant properties of postbiotics play a critical role in neutralizing oxidative stress, which is linked to the progression of chronic diseases. Despite the encouraging insights into their health benefits, we highlight the urgent need for further research to clarify the specific roles of different postbiotic components. A deeper understanding of these mechanisms is essential for developing targeted preventive healthcare applications, and by advancing this knowledge, we aim to create innovative strategies that could significantly enhance health outcomes for at-risk populations. Ultimately, integrating postbiotics into health interventions has the potential to improve preventive care and contribute to the overall well-being of affected individuals and communities.

Enteric microbiota plays a crucial role in the health and productivity of poultry, including influences on nutrient absorption, immune function, and pathogen resistance. In this study, we conducted a genome-wide association study (GWAS) to identify host genetic variants associated with selected bacterial genera found in chickens. We used high-density 600K SNP Affymetrix DNA arrays for genotyping, alongside 16S rRNA gene sequencing to profile caecal microbiota from the same individual chickens. A commercial broiler line (Cobb400, n = 300) and an indigenous (Kadaknath, n = 300) chicken breed from India were investigated, allowing for a comprehensive cross-ecotype analysis. Our analysis identified several host-genetic markers and candidate genes associated with the presence and abundance of specific bacterial genera with known pathogenic or commensal roles, and with specific caecal Enterotypes. Whole-genome sequencing data were then used to further investigate candidate regions around significantly associated variants from the high-density DNA array. Of note, we found markers nearby the genes coding for classical complement activation component C1q, ephrin receptors, and other immunity and inflammatory responses as well as genes coding for products associated with vitamin and co-factor metabolism. The results underscore the impact that host genetics has on the regulation of the gut microbiota and highlights potential pathways through which host genetic variation influences host-bacterial crosstalk and potentially modulates microbial community structure. These findings contribute to the growing understanding of the genetic basis of host-microbiota interactions and offer new avenues for improving poultry health and productivity through selective breeding strategies targeting the microbiome.

Introduction: Although a few bacteria have been studied in great depth, relatively little is known about the characteristics of microbe-microbe interactions that occur within ecosystems on a daily basis. A simple, robust technique was developed to set up the foundation for investigating pairwise bacterial-bacterial interactions, using cell-cell binding as a self-selective mechanism to identify interesting bacterial species pairs.

Methods: Using a Serratia marcescens strain (SMC43) isolated from Georgia soil as a "bait", specific bacteria were purified by their specificity in binding SMC43 bacteria that were themselves attached to a wooden applicator stick.

Results: The isolated Microbial Partners (MiPners) were greatly enriched for members of the genera Sphingobium and Caulobacter. Two streaked MiPners were unable to grow on the plates employed after separation from SMC43to be separated from, and grow on the plate type tested without, SMC43.

Discussion: This suggests that the MiPner technology will be one strategy for purifying bacteria that were previously recalcitrant to culturing.

Saline water drip irrigation is a potential solution for addressing freshwater scarcity in arid regions. However, prolonged use can accumulate soil salinity and reduce phosphorus (P) availability. Biochar and straw amendments have been shown to alleviate these effects, but their mechanisms in regulating microbial genes involved in P transformation under long-term saline irrigation remain unclear. This study aimed to evaluate the impact of biochar and straw incorporation on soil microbial community structure and P availability in saline-irrigated cotton fields. Based on a 14-year field trial, three treatments were developed: saline water irrigation alone (CK), saline water irrigation with biochar (BC), and saline water irrigation with straw (ST). Results indicated that both amendments significantly enhanced soil water content, organic carbon, total P, available P, and inorganic P fractions (Ca₁₀-P, Al-P, Fe-P, and O-P) while reducing soil electrical conductivity and Ca₂-P and Ca₈-P fractions. Biochar increased the relative abundance of Chloroflexi, Gemmatimonadetes, and Verrucomicrobia, while straw promoted Proteobacteria and Planctomycetota. Both treatments decreased the abundance of several P mineralization genes (e.g., phoD, phoA) and increased genes associated with P solubilization (e.g., gcd). Microbial populations and P cycling genes were shown to be tightly associated with soil characteristics, with Ca₂-P and Al-P serving as important mediators, according to correlation studies. Generally, under long-term salty irrigation, biochar, and straw amendments reduced soil salinity, raised soil P availability, decreased the expression of phosphorus cycling-related microbial genes, and improved soil characteristics. These results made them excellent techniques for sustainable soil management.