Biology subjects

Vonaesch, P.

Publications and source records attributed to Vonaesch, P..

5 recordsLinked to original sources

bioRxiv2026

Lithocholic acid modulates the growth of butyrate-producing bacteria and is decreased in the feces of stunted children

Bile acids modulate the intestinal microbiota and serve as key signaling molecules in host physiology. Bile acid dysregulation has been implicated in nutritional and inflammatory diseases; however, data on the pool of bile acids present in stunted children or children suffering of environmental enteric dysfunction (EED) is limited, particularly in the upper intestinal compartment where disease phenotypes are most relevant. In this study, we performed a targeted metabolomics approach on 75 bile acids and their derivatives, including gastric and duodenal aspirates and fecal samples from almost 1000 children from two Sub-Saharan cities. We found that levels of secondary bile acids, especially lithocholic acid, are significantly lower in the feces of stunted and EED children, while ursocholic acid and its derivatives are significantly higher. Levels of primary and sulfated bile acids are also increased in the feces of children with EED. Microbiota sequencing revealed that high lithocholic acid levels are positively associated with butyrate-producing bacteria, while negatively associated with oral taxa like Streptococcus and Veillonella. In vitro tests on a panel of reference strains showed that oral bacteria bioaccumulate and are inhibited by a variety of bile acids, while lithocholic and chenodeoxycholic acids modulate the growth of several butyrate-producing bacteria. This effect was even stronger with tauro- or glycol-conjugated bile acids. Exposing stool-derived in vitro communities from children in Afribiota to these bile acids confirmed their positive impact on butyrate producers and negative effect on overgrowing oral taxa. Our findings suggest that secondary bile acids, reduced in stunting and EED, modulate the growth of butyrate-producing bacteria while suppressing harmful oral taxa, highlighting their potential as tools to modulate microbiota composition.

microbiology↗

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↗

bioRxiv2024

Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation.

Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challenging in vitro resulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.

microbiology↗