Frontiers in microbiomes最新文献

Although microbial community compositions vary throughout the healthy human body, some taxa can be found to reside in multiple anatomical sites. Moreover, some microbiota that have been found to be interconnected, e.g., the gastrointestinal tract and the oral cavity, the female urinary tract and the vagina, the nose (specifically the nares) and the skin. Previously, the urinary microbiome has only been compared to proximal sites; however, several species that inhabit the asymptomatic female urinary tract are also found in distant communities, e.g., Streptococcus mitis, also found in the oral cavity, and Staphylococcus epidermidis, also found in the nares. This prompted our investigation of communities of the oral cavity, nares, and urinary tract, collected from the same individual. In this study, we profiled the oral, nasal, and urinary microbiomes of 26 self-identified "healthy" female participants using 16S rRNA amplicon sequencing. The urinary microbiome was found to be distinct from the oral and nasal communities. Nevertheless, Actinomyces, Corynebacterium, Escherichia + Shigella, Lawsonella, Staphylococcus, and Streptococcus were found to be present within communities of all three anatomical sites. Genera predominant within the oral and nasal communities were often low-abundant taxa within the urinary microbiome. To date, comparisons of the urinary microbiome to microbiomes of other anatomical sites is limited. The distinction between the urinary microbiome and that of the more distant oral and nasal site highlights the role that the environment plays in shaping these communities.

Background: Whether domestication, post-domestication spread, and breeding affected the maize leaf endosphere microbiota is poorly understood despite the well-known effects of those processes on the crop's genetics and responses to the environment. We examined the leaf endosphere microbial communities associated with three plant groups (Zea mays): teosintes, maize landraces, and maize elite inbreds. The teosintes group included Balsas (Z. mays parviglumis) and perennial (Zea diploperennis) teosinte, and each maize (Z. mays mays) group included genotypes from Mexico and USA. We used 16S-V4 region amplicon sequencing of the leaf endophytic microbiota to infer how the microbial communities of inbred maize may have been shaped by the crop's evolution, and whether they were affected by: (i) the transition from a perennial life history to an annual life history in the teosintes; (ii) domestication of maize from Balsas teosinte; (iii) northward spread of landrace maize from Mexico to the US; and (iii) breeding of landrace maizes to produce elite inbreds.

Results: The leaf endophytic microbial community differed among the plant groups and genotypes, and was affected by domestication, as indicated by a decline in bacterial diversity and changes in microbial community structure between wild (teosinte) and domesticated (maize) Zea. While the microbial community structure was stringent and regulated in the teosintes, it was variable in the maize landraces and inbreds, as evidenced by greater distances to centroid based on Euclidean dissimilarity metric. This pattern was suggestive of microbial dysbiosis in the leaf endosphere associated with domestication and is consistent with predictions of the Anna Karenina principle. This finding marks the first evidence of dysbiosis associated with domestication. FAPROTAX predictions suggested that the teosintes may harbor microbial communities enriched in taxa associated with cellulolytic, chitinolytic, and nitrate respiration functions, while the maizes showed higher fermentation and nitrate reduction functions.

Conclusions: Our results showed that the leaf endosphere microbial community structures in maize are consistent with alterations associated with dysbiosis. Our findings enhanced our understanding of the effects of anthropogenic processes including crop domestication, spread, and breeding on the leaf endosphere of elite maize cultivars, and may guide the development of evolutionarily-and ecologically sustainable biofertilizers and biocontrol agents.

The phylum Acidobacteriota is ubiquitous and a dominant bacterial group in arid lands, playing a crucial role in nutrient cycling and ecosystem functioning. This study explores Acidobacteriota in Southern African arid lands through two complementary approaches. A meta-analysis of 240 soil samples revealed relative abundances ranging from 0.008% to 39.1%, with pH identified as the primary driver of community variance. In addition, 96 bulk soil samples from the Nama Karoo were analyzed using full-length 16S rRNA gene sequencing (V1-V9). Acidobacteriota abundance ranged from 2.3% to 12.2%, with Subdivisions 3, 4, and 6 being the most dominant, while rare subdivisions, such as 2 and 9, showed location-specific distributions. Significant beta-diversity differences (p = 0.002) were linked to soil moisture, electrical conductivity, and nitrate availability, and some subdivisions exhibited correlations with organic carbon and nitrate. Co-occurrence patterns with Planctomycetota and Armatimonadota suggest potential biofilm formation and shared ecological niches. This study provides the first comprehensive assessment of Acidobacteriota in Southern African arid lands, highlighting dominant and rare subdivisions, localized ecological associations, and the need for future work on their metabolic functions and adaptive strategies in arid ecosystems.

Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.

Background/aim: The increasing incidence of early-age-onset colorectal neoplasia (EAO-CRN) in individuals under 50 years old poses a global health concern. This study aimed to investigate the variations in the microbiota in individuals with EAO-CRN compared with a control group, utilizing stool, oral swab, and saliva samples.

Methods: Participants under 50 years of age provided stool, oral swab, and saliva samples. Colorectal neoplasia was classified into the serrated lesions and adenoma-carcinoma groups based on histology and compared with a control group without polyps. The alpha diversity and the taxonomic abundance differences were assessed using amplicon sequence variants obtained through 16S rRNA sequencing and matched taxonomy data.

Results: A total of 45 participants were included: 14 in the control, 13 in the serrated lesions, and 18 in the adenoma-carcinoma groups. Microbial analysis revealed no significant differences in the alpha diversity among the groups. However, the stool samples from the serrated lesions group had higher levels of the families Erysipelotrichaceae and Lachnospiraceae compared with the control group. Analysis of the oral swabs indicated relatively elevated levels of the family Streptococcaceae in both the serrated lesions and adenoma-carcinoma groups. In the saliva samples, the serrated lesions and adenoma-carcinoma groups showed higher levels of the family Lactobacillaceae, with the serrated lesions group also exhibiting elevated levels of the family Bifidobacteriaceae.

Conclusions: This study elucidates the microbiota changes associated with EAO-CRN, distinguishing between serrated lesions and adenoma-carcinoma groups using stool, oral swab, and saliva samples. These findings contribute to the understanding of the relationship between microbiota and colorectal neoplasia in the early-onset population.

Background: The human milk microbiota significantly contributes to the shaping of the infant gut microbiota during early life. Influenced by maternal factors such as birth mode, diet, and breastfeeding practices, these microbial communities are critical for infant health. We explored the effect of maternal human immunodeficiency virus (HIV) status and breastfeeding practices on breast milk microbiota composition and its correlation with infant gut microbiota between 7 and 14 days postpartum.

Methods: Breast milk and stool microbiota from 68 lactating HIV-infected and uninfected women and their 69 infants (including one set of twins) were characterized using 16S rRNA gene sequencing. Sociodemographic and clinical data were also collected.

Results: Breast milk microbiota was dominated by Streptococcus and Gemella, whereas the infant gut microbiota showed a co-occurrence of early colonizers such as Enterobacteriaceae_unclassified, Bifidobacterium, and Streptococcus. In contrast, maternal stool exhibited greater microbial diversity, enriched in Romboutsia and Clostridium_sensu_stricto_1. Small, non-significant differences were observed in alpha diversity by maternal HIV status (Cohen's d ≈ -0.38; 95% CI: -3.88 to 0.07), suggesting possible modest to no effects, even though p-values were not significant. Clostridium_sensu_stricto_1 was more abundant in HIV-uninfected mothers. Infant HIV exposure and maternal antibiotic prophylaxis had no detectable effect on gut microbiota diversity or composition. Notably, positive correlations were observed between breast milk and infant gut taxa abundances, including Gemella (ρ = 0.33, p = 0.010) and Enterobacteriaceae_unclassified (ρ = 0.31, p = 0.016). SourceTracker analysis indicated that 31.5% of infant gut taxa were traceable to breast milk, with higher contributions in HIV-exposed infants (41%) compared with HIV-unexposed infants (25.6%).

Conclusion: This study is among the first to investigate breast milk microbiota in the context of HIV infection in Zimbabwe. We demonstrated that maternal HIV infection and cotrimoxazole prophylaxis did not measurably alter breast milk or early infant gut microbiota composition. Despite limited statistical power to detect small-to-moderate effects, taxa-level correlations and microbial source tracking supported breast milk as a major contributor to early gut colonization. These results underscore breast milk-mediated microbial seeding in early life, while highlighting the need for larger longitudinal studies to define how maternal HIV status may subtly influence vertical microbial transfer.

The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.

Polycystic ovary syndrome (PCOS) is a multifaceted endocrine and metabolic disorder intricately associated with hyperandrogenism (HA), insulin resistance (IR), chronic inflammation, and obesity. The gut microbiota (GM) is considered a mature endocrine organ capable of exerting multiple effects by regulating bile acids (BAs) metabolism. Disruption of GM homeostasis can initiate various pathological processes, including metabolic disorders, endocrine imbalances, low-grade inflammation, and reduced insulin sensitivity, thereby providing novel avenues for research into the pathogenesis of PCOS. There is bidirectional signalling between the GM and BAs: the microbial community tightly regulates the metabolism and synthesis of BAs, while the BAs pool and its composition affect the diversity and homeostasis of intestinal microorganisms. Dysregulation of BAs metabolism mediated by the GM may constitute a crucial pathological link in the progression of PCOS. The objective of this review is to investigate the function of BAs as a signalling molecule bridging the GM and PCOS, to synthesise the current understanding of the roles of BAs and intestinal microorganisms in the pathogenesis of PCOS, and to explore new treatment strategies for PCOS further.

The human gut microbiome has emerged as a pivotal modulator of brain function and mental health, acting through intricate bidirectional communication along the gut-brain axis. Mounting evidence suggests that microbial communities influence neurodevelopment, neurotransmission, and behavior via pathways involving the vagus nerve, immune signaling, and microbiota-derived metabolites such as short-chain fatty acids and neurotransmitter precursors. This review critically examines the mechanistic underpinnings of microbiota-brain communication and evaluates current findings linking dysbiosis to psychiatric conditions, including depression, anxiety, schizophrenia, autism spectrum disorder, and bipolar disorder. In addition, it assesses the therapeutic potential of microbiome-targeted interventions-such as probiotics, fecal microbiota transplantation (FMT), and precision dietary modulation-in ameliorating neuropsychiatric symptoms. While the field holds considerable promise, limitations, including correlational study designs, small sample sizes, and a lack of standardized methodologies, underscore the need for rigorous, large-scale clinical trials. A deeper understanding of host-microbe interactions may catalyze a paradigm shift in psychiatric treatment, paving the way for novel, personalized microbiome-based therapeutics.