Biology subjects

Teo, Y.

Publications and source records attributed to Teo, Y..

3 recordsLinked to original sources

bioRxiv2026

Phage Endolysin Enables Targeted Manipulation of the Small Intestinal Microbiota and Uncovers Niche Overlap Between Oral and Butyrate-Producing Taxa

Oral bacterial overgrowth in the small intestine has been associated with dysbiosis, impaired nutrient absorption, and stunted growth in undernourished children, a condition referred to as small intestinal oral bacterial overgrowth (SIOBO). Here, we explore the use of a phage-derived lysin as a precision antimicrobial to selectively target Streptococcus salivarius within complex microbial communities. Through a newly developed, medium-throughput bioinformatic and wet-lab pipeline we identified, cloned and produced a prophage-encoded lysin from S. salivarius and demonstrated its potent and specific lytic activity against a panel of 49 clinical S. salivarius strains from stunted children, while sparing related species such as S. mitis, S. parasanguinis and S. thermophilus. Application of the lysin to human stool-derived in vitro communities and to mice colonized with S. salivarius led to an approximate 2-3 log reduction in S. salivarius abundance while preserving overall bacterial community composition. However, we observed a negative correlation between S. salivarius and Coprococcus comes in vitro, and Eubacterium xylanophilum, Akkermansia, Lactobacillus and Ruminococcus in vivo. Spent medium assays confirmed niche overlap between 10 clinical strains of S. salivarius and 28 different taxa involved in butyrate production. Together, these results suggest that phage-derived lysins can offer multiple benefits by selectively removing ectopically colonized oral taxa and indirectly promoting beneficial anaerobes.

microbiology↗

bioRxiv2025

Strain-level translocation and enrichment mechanisms of oral bacteria in the lower gastrointestinal tract of stunted children

Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal and fecal samples, and isolation and whole genome sequencing of 87 Streptococcus salivarius isolates, we showed translocation of members of the genera Streptococcus, Veillonella, Rothia and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, suggesting a source-sink dynamic in which S. salivarius populations are continuously seeded from the oral cavity without durably establishing in the lower gastrointestinal tract. Last, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is due to increased biomass, while in the colon it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies mechanisms of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.

microbiology↗

bioRxiv2025

Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota

The gut microbiome plays a fundamental role in human health, prompting efforts to catalogue and preserve its diversity across human populations. While DNA sequencing dominates microbiome research, cultivation remains essential for mechanistic studies and therapeutic development. Yet, best practices for long-term stool preservation remain limited. Here, we compared the stability of eight cryopreservation treatments for maintaining viable stool microbiota over a 1-year storage period at -80{degrees}C (freezer) or at -196{degrees}C (liquid nitrogen), using samples from infants, children, and adults. Combining cultivation on six media with 16S rRNA sequencing, we show that ultralow temperature cryopreservation has minimal impact on microbiota diversity compared to fresh cultures. Standard glycerol preservation and simple snap-freezing performed comparably to more complex and costly protocols, with all cultured samples retaining donor-specific microbiota profiles also after long-term cryopreservation. The lack of strong treatment-specific effects on microbiota composition suggest a shared microbial response to freeze-thaw stress favoring fast-growing taxa. Our findings offer practical, low-cost strategies for stool biobanking. ImportanceThe cultivation of bacterial taxa from complex communities, such as those in fecal samples, is essential for mechanistic studies and the development of microbiota-based therapeutics, including defined consortia and individual probiotic strains. Such cultivation efforts typically rely on previously stored samples; however, systematic knowledge regarding long-term preservation strategies that ensure viability and regrowth of constituent bacterial taxa remains limited. In this study, we systematically evaluated 16 distinct cryopreservation conditions to assess their efficacy in maintaining bacterial viability. Our results show that conventional glycerol-based preservation and simple snap-freezing are comparable in performance to more elaborate and cost-intensive protocols. Moreover, we identified the duration of sample transport prior to freezing as a critical determinant of post-thaw bacterial recovery. These findings provide valuable data on the relative effectiveness of various preservation methods and support the use of low-cost, easily implementable strategies that are particularly suitable for application in resource-limited settings.

microbiology↗