Biology subjects

Seki, D.

Publications and source records attributed to Seki, D..

4 recordsLinked to original sources

bioRxiv2025

Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments

Primer bias in 16S rRNA gene amplicon sequencing can distort microbial diversity estimates by underrepresenting key taxa. We introduce a modified primer pair (V4-EXT) targeting the hypervariable V4 region of bacterial and archaeal 16S rRNA genes, with improved in silico taxonomic inclusivity. To benchmark performance, we analyzed 938 samples from terrestrial, aquatic, and host-associated habitats, comparing microbial community profiles derived with V4-EXT and the currently most widely used V4-targeted primers. V4-EXT substantially improved the detection of Patescibacteria and other underrepresented lineages, such as Chloroflexota and Iainarchaeota, while enhancing recovery of novel amplicon sequence variants across sample types. Overall, V4-EXT provides broader taxonomic coverage and more inclusive microbial community profiles, particularly in high-diversity ecosystems such as groundwater and soils. We propose V4-EXT as a robust successor for comprehensive microbial community analysis across diverse habitats.

microbiology↗

bioRxiv2025

Mutualistic interactions between Escherichia coli and Bifidobacterium bifidum enable degradation of human milk oligosaccharides in healthy infants

The development of the human gut microbiota during infancy is marked by frequent colonization of Enterobacteriaceae, a bacterial family notoriously associated with various diseases. Yet, despite their prominence in the absence of illness, their exact ecological role during healthy maturation of the infant gut remains poorly explored. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed neonates (n=41) at two, six, and eleven months post-delivery, as well as microbiota of related mothers (n=30) with shotgun metagenomic sequencing, complemented by novel computational approaches and experimentation. Strain-resolved profiling indicates that dominant Bifidobacterium are frequently shared between infants and parenting mothers, while Escherichia coli originate from other sources, yet often persist within individuals. Despite their ecological differences, these genera co-exist, and both display evolutionary adaptations related to the utilization of human milk oligosaccharide (HMO) degradation products. We demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating the cooperative degradation of 2'-fucosyllactose (2'FL), the predominant HMO. In turn, the liberated monosaccharides support E. coli proliferation and niche occupation. These findings reveal a fundamental cross-feeding interaction during development of healthy infant gut microbiota.

microbiology↗

bioRxiv2025

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Animal hosts harbour divergent microbiota, including various Bifidobacterium species and strains, yet their evolutionary relationships, and functional adaptions remain understudied. By integrating taxonomic, genomic and predicted functional annotations, we uncover how Bifidobacterium adapts to host-specific environments, shaped by vertical transmission, dietary influences, and host phylogeny. Our findings reveal that host phylogeny is a major determinant of gut microbiota composition. Distinct microbial networks in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, we identify strong co-phylogenetic associations between Bifidobacterium strains and their hosts, driven by vertical transmission and dietary selection, underscoring the intricate co-evolutionary dynamics between these microbes and their hosts. Functional analyses highlight striking host-specific metabolic adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, we observe an enrichment of glycoside hydrolases (GH) tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 -amylases featuring diverse carbohydrate-binding modules (CBM25, CBM26, and the novel CBM74). These adaptations emphasise the ecological flexibility of Bifidobacterium in breaking down -linked glucose polysaccharides, such as resistant starch. Together, our study provides new insights into the evolutionary trajectories and ecological plasticity of Bifidobacterium, revealing how host phylogeny and dietary ecology drive microbial diversity and function. These findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.

microbiology↗

bioRxiv2023

Characteristics of putative keystones in the healthy adult human gut microbiome as determined by correlation network analysis

Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. IMPORTANCEThe work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance. By employing a robust workflow based on bootstrapping and subsampling techniques, we identify putative keystone species at the genus and species level. This emphasizes the importance of considering taxonomic resolution when investigating correlations. The potential impact of keystones on community stability provides valuable insights for systematic microbiome manipulation. Furthermore, the observed clusters of co-occurring taxa align well with recent findings and emphasize the reproducibility and relevance of the identified patterns in microbial community composition. We are able to add a functional dimension to the analysis with the identification of distinct transcriptional states in putative keystone taxa, highlighting their functional versatility and adaptability.

microbiology↗