Microbiome research reports最新文献

Background: While extensive research exists on the human microbiome, a number of outstanding questions remain regarding the infant microbiome in the initial stages of life. This study aimed to determine the timing of very early microbial colonization in humans, assess the contribution of maternal microbial sources to their offspring and examine the effects of perinatal factors such as delivery mode, gestational age, and feeding practices on the maternal and infant microbiota in early life. Methods: Using a cohort of 18 healthy mother-infant dyads, maternal saliva (within 24 h postpartum), vaginal (1 h prepartum), and placental (1 h postpartum) samples were collected. From their corresponding infants, saliva (within 24 h postpartum) and meconium (within 96 h postpartum) samples were collected. 16S rRNA amplicon sequencing was utilized to assess the taxonomic and inferred functional compositions of the bacterial communities from both mothers and infants. Results: Our results consolidate and corroborate recent findings addressing the existence of a meconium microbiome and the absence of a placental microbiome. We show that significant sharing of microbiota, primarily Streptococcus and Veillonella species, between the maternal oral cavity and the infant oral cavity occurs in early life. Perinatal factors such as vaginal delivery and exclusive breastfeeding were strongly associated with enhanced microbial richness and diversity in infants. Conclusions: This study provides information on the relationship between health and delivery factors and the first establishment of the infant microbiota. These findings could offer valuable guidance to clinicians and mothers in optimizing the infant microbiota toward health during infancy and later life.

Aim: To evaluate the effectiveness of marine-sourced bacterial DNA spike-in quantification for determining absolute microbial abundance in the gut microbiome of mother-infant pairs and to compare this method with conventional quantification techniques. Methods: We conducted a pilot study involving six mother-infant pairs, applying a DNA spike-in quantification method using bacterial DNA from Pseudoalteromonas sp. APC 3896 and Planococcus sp. APC 3900, isolated from deep-sea fish. We compared our approach with established absolute quantification methods - flow cytometry, total DNA measurement, quantitative PCR (qPCR), and culture-based plate count - to evaluate microbial load and taxonomic composition across mother-infant samples. Results: Our spike-in method accurately estimated microbial loads, producing results consistent with qPCR and total DNA quantification. We observed that mothers exhibited higher total bacterial loads than infants by approximately half a log, while the abundance of Bifidobacterium was comparable in both groups. The spike-in method revealed significant differences in taxonomic composition, highlighting the impact of absolute quantification on microbiome analysis outcomes. Importantly, the method did not alter alpha diversity measures but slightly affected beta diversity analysis, reflecting more precise inter-group differences. Conclusion: Marine-sourced bacterial DNA spike-in offers a reliable, scalable, and accurate approach for absolute microbiome quantification. This method enhances microbiome analysis by addressing biases inherent in relative abundance measures, providing a deeper understanding of microbial dynamics in mother-infant gut microbiomes.

Aim: The human gastrointestinal tract is home to a complex and dynamic microbial community, known as the gut microbiota, which begins to form at birth and evolves throughout life. Among the factors influencing its initial development, breastfeeding is one of the most important. Human milk is a chemically complex body fluid, including hormones, like melatonin, which is involved in regulating the sleep-wake cycle, helping to establish the newborn's circadian rhythm. In the current study, the molecular interactions between human melatonin and a bifidobacteria-rich infant gut microbiota were explored. Methods: Possible molecular communication was assessed using in vitro assays and functional genomic approaches. Results: Our results highlight that melatonin elicits different functional microbial impacts, both at transcriptional and phenotypic levels (i.e., adhesion to intestinal cells), that are dependent on the bifidobacterial species analyzed. Conclusion: Among the bifidobacterial taxa assayed, Bifidobacterium bifidum demonstrated the highest level of molecular interaction with melatonin, highlighting its significant role in this process.

Aim: Choline is a universal methyl group donor, playing an essential role in DNA methylation, signaling pathways, and the transport and metabolism of lipids. The primary source of choline intake is diet, and chronic deficiency has been associated with dementia, cardiovascular disease, and liver disease. Choline bioavailability can be diminished by gut microbes that express choline trimethylamine-lyase (cutC), an enzyme that converts choline into trimethylamine (TMA), a precursor for TMA N-oxide (TMAO), which is associated with an increased risk of cardiovascular diseases. Gut microbiota modulation can be achieved by prebiotics such as galactooligosaccharides, inulin, and fructooligosaccharides. The aim of our study is to use choline with prebiotics to modulate the gut microbiota to enhance choline bioavailability and minimize TMA production. Methods: We employed an ex vivo microcosm system consisting of healthy human stool samples with choline and different prebiotics and measured TMA and choline levels by targeted metabolomics. Shotgun metagenomic profiling was also performed to investigate alternation in gut microbiota composition during choline and prebiotic interventions. Results: Our study showed that choline to TMA conversion is dependent on a choline derivative and supplementing galactooligosaccharides (GOS) reduces this conversion. Choline to TMA conversion was associated with enriched microbiota from the genus Dialister, whereas GOS supplementation led to an increase in Blautia and a reduction in Clostridia populations. Loss of Clostridia also reduced a subset of Clostridium species, Clostridium citroniae, known to encode the cutC gene. The abundance of Dialister enhanced the chorismate biosynthesis pathway, while a reduction in Clostridium supported tryptophan and methionine pathways. Conclusion: This study is the first to identify the combination of choline and GOS supplementation as a potential strategy to modulate gut microbiota and its metabolites in order to improve disease etiology.

The initial gut colonization of the infant plays a pivotal role in shaping the immune system, developing the intestinal tract, and influencing host metabolism, all of which are strongly influenced by several determinants, such as gestational age at birth, mode of delivery, neonatal feeding practices, early-life stress (ELS), and exposure to perinatal antibiotics. However, resulting gut microbiome (GM) dysbiosis may alter this developmental programming, leading to long-term adverse health outcomes. This narrative review synthesizes current knowledge on early-life GM development and its long-term impact on health. Specifically, it addresses how early-life GM dysbiosis may affect the trajectory of physiological processes, predisposing individuals to conditions such as allergic diseases, metabolic disorders, type 1 diabetes, inflammatory bowel disorders, and atherosclerotic cardiovascular diseases. In addition, it examines the influence of probiotic and prebiotic supplementation during pregnancy and early life in shaping infant GM composition, as well as the impact of ELS-induced GM dysbiosis on mental health. Recent research suggests that the early-life microbiota initiates long-lasting effects, and inadequate or insufficient microbial exposure triggers inflammatory responses associated with several physiological conditions. Although several studies have reported a connection between ELS and the GM during both prenatal and postnatal periods, a unified microbiome signature linked to either prenatal or postnatal stress remains to be fully elucidated. Thus, future studies are needed to establish causality and determine whether modifiable factors affecting the GM could be targeted to improve gut health, especially in children exposed to contextual stress or adverse conditions.

Aim: Wolbachia species are among the most abundant intracellular endosymbionts of insects worldwide. The extensive distribution of Gram-negative Wolbachia among insects highlights their evolutionary success and close relationship with many insect host species. This study aimed to characterize a novel Wolbachia strain from the Wild Lime Psyllid, Leuronota fagarae (L. fagarae), to understand its evolutionary relationship with Wolbachia from psyllid pests like Diaphorina citri, the vector of Huanglongbing (HLB). Methods: Wild-caught L. fagarae colonies from Florida, USA, were maintained on Zanthoxylum fagara. RNA was extracted from the salivary glands, heads, and whole bodies of male and female adult L. fagarae. Four cDNA libraries were sequenced using short read technology and de novo transcriptome assembly was performed. Multilocus sequence typing (MLST) of nine conserved loci and wsp gene analysis classified the strain's phylogeny, while sequence mapping and functional annotation provided insight into host-microbe interactions. Results: The new Wolbachia strain, designated Wolbachia endosymbiont of Leuronota fagarae (wLfag-FL), was assigned to supergroup B, showing relation to Wolbachia strains of other related psyllids. Transcriptome analysis identified 1,359 Wolbachia transcripts with 465 assigned functions encompassing metabolic and secretion system pathways. Ankyrin domain proteins and a partial bacterioferritin sequence were detected, suggesting nutritional provisioning roles. Conclusion: The characterization of wLfag-FL expands the known Wolbachia host range and informs HLB-related pest biology. Its phylogenetic placement and transcript annotations offer insights into symbiotic interactions, potentially guiding environmentally safe pest control strategies targeting psyllid fitness and pathogen transmission.

The incidence of locally advanced rectal cancer (LARC) among young people is rising alarmingly. In recent years, new protocols have been introduced for the management of LARC, some of which are associated with the risk of significant toxicity. Despite these advancements, robust predictive biomarkers for LARC have yet to be established. The microbiome has emerged as a potential biomarker due to its interaction with tumor multiomics. This article provides a critical overview of the current evidence on the microbiome and LARC, including its relationship with the immune system and epigenomics, and also highlights both the current limitations and future perspectives in the field.

Maternal milk contains its own diverse microbiome, which has been hypothesized to colonize the infant gut during breastfeeding; however, the dynamics of this process are not well understood, particularly among very-low-birth-weight (VLBW) infants. A recent study published in Cell Reports Medicine by Shama et al. identifies novel dose-dependent relationships between maternal milk microbiota and infant gut microbiota in a cohort of VLBW infants and further explores the potential impact of infant feeding practices and antibiotic use on these microbial colonization dynamics.

Microbial communities inhabiting various body sites play critical roles in the initiation, progression, and treatment of cancer. The gut microbiota, a highly diverse microbial ecosystem, interacts with immune cells to modulate inflammation and immune surveillance, influencing cancer risk and therapeutic outcomes. Local tissue microbiota may impact the transition from premalignant states to malignancy. Characterization of the intratumoral microbiota increasingly reveals distinct microbiomes that may influence tumor growth, immune responses, and treatment efficacy. Various bacteria species have been reported to modulate cancer therapies through mechanisms such as altering drug metabolism and shaping the tumor microenvironment (TME). For instance, gut or intratumoral bacterial enzymatic activity can convert prodrugs into active forms, enhancing therapeutic effects or, conversely, inactivating small-molecule chemotherapeutics. Specific bacterial species have also been linked to improved responses to immunotherapy, underscoring the microbiome's role in treatment outcomes. Furthermore, unique microbial signatures in cancer patients, compared with healthy individuals, demonstrate the diagnostic potential of microbiota. Beyond the gut, tumor-associated and local microbiomes also affect therapy by influencing inflammation, tumor progression, and drug resistance. This review explores the multifaceted relationships between microbiomes and cancer, focusing on their roles in modulating the TME, immune activation, and treatment efficacy. The diagnostic and therapeutic potential of bacterial members of microbiota represents a promising avenue for advancing precision oncology and improving patient outcomes. By leveraging microbial biomarkers and interventions, new strategies can be developed to optimize cancer diagnosis and treatment.

MicroRNAs (miRNAs) are short, non-coding RNAs that play gene expression regulatory roles in eukaryotes. MiRNAs are also released in body fluids, and in the intestine, they are found in the lumen and feces. Here, together with exogenous dietary-derived miRNAs, they constitute the fecal miRNome. Several miRNAs were identified in the feces of healthy adults, including, as shown here, core miRNAs hsa-miR-21-5p and hsa-miR-1246. These miRNAs are important for intestinal homeostasis. Recent evidence suggests that miRNAs may interact with gut bacteria. This represents a new avenue to understand host-bacteria crosstalk in the gut and its role in health and disease. This review provides a comprehensive overview of current knowledge on fecal miRNAs, their representation across individuals, and their effects on the gut microbiota. It also discusses existing evidence on potential mechanisms of uptake and interaction with bacterial genomes, drawing from knowledge of prokaryotic small RNAs (sRNAs) regulation of gene expression. Finally, we review in silico and experimental approaches for profiling miRNA-mRNA interactions in bacterial species, highlighting challenges in target validation. This work emphasizes the need for further research into host miRNA-bacterial interactions to better understand their regulatory roles in the gut ecosystem and support their exploitation for disease prevention and treatment.