Biology subjects

Forslund-Startceva, S. K.

Publications and source records attributed to Forslund-Startceva, S. K..

6 recordsLinked to original sources

bioRxiv2026

A nutrient-derived dietary gradient links gut microbiome composition, network structure, and host physiology

Diet is an important determinant of gut microbiome composition and host physiology. However, dietary exposure is often represented using categorical groups that may not fully capture variation in nutrient intake or its associations with gut microbiome and host biomarkers. Here, we analyzed diet-microbiome-host physiology relationships in healthy adults with long-term adherence ([≥]2 years) to omnivore, vegetarian, or vegan diets. We integrated four-day weighed dietary records, blood biomarkers, and 16S rRNA gene sequencing to characterize dietary intake, host physiology, and gut microbiome composition. We derived nutrient intake gradients by dimensionality reduction of representative nutrients and identified the second nutrient intake gradient (NIG2) as a quantitative axis reflecting variation between animal- and plant-leaning nutrient profiles, broadly recapitulating categorical dietary groups. While NIG2 showed no association with microbiome within-sample diversity, it explained gut microbiome compositional variation that was not detected using categorical dietary groups. Mediation analyses identified nominal candidate microbiome-mediated diet-biomarker relationships involving thyroid-related, hematological, and vitamin-related biomarkers. Network analyses of NIG2-defined animal-leaning and plant-leaning subsets identified subset-specific microbial associations and differences in microbial community structure and potential interactions. Overall, this continuous nutrient-derived dietary gradient provides a quantitative exposure metric for characterizing diet-microbiome-host physiology relationships. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/740531v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@104a825org.highwire.dtl.DTLVardef@bb2b33org.highwire.dtl.DTLVardef@114171org.highwire.dtl.DTLVardef@df9c38_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Anthropogenic land use exerts selection pressures on the resistome of a wild rodent

Antimicrobial resistance poses a significant global health challenge. However, the factors maintaining antimicrobial resistance genes (ARGs) in wildlife microbiomes remain unclear particularly in species inhabiting human-dominated landscapes. We analysed 875 gut metagenomes from wild house mice (Mus musculus) on German farms between 2016 and 2022 to identify environmental and host determinants of ARG occurrence. Using joint species distribution models, we quantified the influence of landscape, climate and mouse associated characteristics on the occurrence of individual ARGs and on trait dependence among genes. Environmental variables and livestock farming intensity explained more than 21% of ARG variation, whereas host characteristics accounted for less than 10%. Analysis of ARG traits revealed that agricultural land use and exposure to livestock increased the occurrence of mobile ARGs. Pig density was strongly associated with integron-encoded sulfonamide resistance genes and genes conferring tetracycline and beta-lactam resistance. Consistent with these findings, mouse resistomes closely resembled those of livestock manure. Taken together, our results show that landscape conditions, particularly farming intensity, shape the distribution of specific ARGs and mobile ARGs in house mice microbiomes. Understanding the factors impacting ARGs prevalence in wildlife is crucial for determining transmission of antimicrobial resistant microorganisms from animal and environmental reservoirs.

microbiology↗

bioRxiv2025

Global analysis of infant gut microbiota revealed distinctive maturation dynamics across lifestyles

The infant gut microbiome develops during the first years of life and influences long-term health through its interaction with immune system development. However, our understanding of early-life microbiome assembly is biased by the predominance of infants with industrialized lifestyles from North America and Europe. Here, we address this bias by assembling a globally representative dataset of infant gut microbiomes to train a microbiome maturation model that can characterize lifestyle specific patterns of microbial maturation as a function of age. Models trained exclusively on industrialized infants perform poorly when applied to non-industrialized datasets. In contrast, more diverse models including individuals from both lifestyles achieve increased correlation between microbial and chronological age. We identified differences in relevant taxa associated with the maturation in the different lifestyles. Additionally, our modeling approach detects a delay in the microbial maturation of independent cohorts of severely malnourished and preterm infants compared to healthy ones. Our results underscore the relevance of global diversity in microbiome research and provide deeper insights into context-dependent maturation dynamics of the infant gut microbiome.

microbiology↗

bioRxiv2025

Similar Fecal SCFA Patterns Despite Diverse Gut Microbiota in Polish and Japanese Children During the First Two Years of Life. The longitudinal, comparative, validated study.

BackgroundEarly-life gut microbiome assembly is shaped by environment, diet, and perinatal exposures. Whether population context shifts taxonomic trajectories and functional outputs similarly remains unclear. MethodsWe re-analyzed longitudinal infant cohorts from Poland (PL) and Japan (JP) across five time points (1 week, 1 month, 6 months, 1 year, 2 years). Amplicon sequence variants (ASVs) were processed uniformly. Cross-sectional alpha diversity (richness, evenness, Shannon, Simpson) was modeled with covariate adjustment (sex, antibiotics, diet). Beta diversity used Bray-Curtis distances (PCoA) and PERMANOVA (unadjusted/adjusted). Confounder-aware genus-level differential abundance identified features not reducible to covariates. Longitudinal genus trajectories and genus-SCFA (acetate, propionate, butyrate, isobutyrate) associations were tested using mixed-effects models. SCFAs were z-score-normalized to harmonize units across cohorts. Sensitivity analyses restricted PL to vaginally delivered infants. Finnish (FIN) and United States (US) cohorts were included for taxonomic validation. ResultsEvenness, Shannon, and Simpson were similar between PL and JP at most time points; richness was higher in PL at 1 week with trends at 6 months. Beta diversity showed a significant country effect at every time point except 1 month, robust to covariate adjustment and to restriction to 74 genera shared between PL and JP. Genus-level differential abundance yielded 33 features (26 enriched in PL, 7 in JP) without consistent cross-time recurrence. Longitudinally, most genus trajectories were cohort-specific; genus-SCFA associations were largely population-specific (few overlaps for butyrate/isobutyrate, none for acetate/propionate). Despite taxonomic and association differences, SCFA trajectories did not differ between cohorts after harmonization and adjustment. FIN/US validation supported the robustness of temporal taxonomic signals with few discordances. ConclusionsTaxonomic profiles and genus-SCFA relationships diverge across populations, whereas core metabolic outputs (fecal SCFAs) follow a conserved, resilient trajectory in early life. This "divergent taxa, convergent function" pattern suggests early-life interventions should prioritize functional maturation over targeting specific taxa. Broader multi-omic studies integrating growth, immune, and neurodevelopmental outcomes are warranted.

microbiology↗

bioRxiv2025

Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol.

Antibiotic resistance poses a global public health threat. Cefiderocol, a recently introduced siderophore cephalosporin, employs a "Trojan Horse" mechanism by exploiting bacterial iron uptake systems for cell entry. Yet, resistant clinical isolates are already observed in clinics and resistance mechanisms are difficult to characterize. Here, we applied functional metagenomics to identify cefiderocol resistance genes. Functional metagenomic DNA libraries from diverse environmental samples collected across several countries were expressed in a cefiderocol-sensitive Escherichia coli host. This yielded four resistant clones with DNA originating from wastewater or freshwater DNA libraries. The identified antibiotic resistance genes (ARGs) causing an increase in cefiderocol minimum inhibitory concentrations encoded for beta-lactamases (VEB-3, OXA-372 homolog and YbxI homolog) and a partial penicillin binding protein homolog. Three of four shared closest homologs in pathogenic bacteria. One ARG was associated with a mobile genetic element and was broadly distributed across all wastewater samples from every country surveyed. This study underscores the critical importance of environmental surveillance for ARGs, particularly for novel agents like cefiderocol with limited understanding of resistance mechanisms.

microbiology↗

bioRxiv2024

Baseline microbiome composition impacts resilience to and recovery following antibiotics

The gut microbiome of healthy individuals naturally undergoes temporal changes linked to the dynamics of its community components1. These dynamics are only observable in longitudinal studies; they are particularly relevant to understanding ecosystem responses to external environment disturbances. External exposures, such as antibiotic treatment, significantly reshape the gut microbiome, impacting both pathogen and commensal microbes2. The gut microbiome plays pivotal roles in digestion, nutrient absorption, and mental health, influencing immune systems, obesity, and various diseases3-6. Consequently, beyond the short-term effects on the host gut microbiome dynamics, alterations resulting from antibiotic exposure also have enduring repercussions on human health and physiological equilibrium7. Therefore, enhancing gut microbiome resilience during antibiotic treatment is essential, with the goal of mitigating prolonged adverse effects. Here, we explored the impact of pre-antibiotic microbial and functional profiles on resilience, suggesting that specific baseline features exhibit greater resilience to antibiotics-induced changes. Our results identified an uncultured Faecalibacterium prausnitzii taxon as a species at baseline associated with diminished resilience. We demonstrated that this association could be linked to the role of this F. prausnitzii taxon as a keystone species. Additionally, we observed the influence of other commensal bacteria, such as Bifidobacterium animalis and Lactobacillus acidophilus, as well as functional modules, such as multidrug resistance efflux pump, on resilience. This lays the foundations for designing targeted strategies to promote a resilient gut microbiome before antibiotic treatment, alleviating possible prolonged effects on human health.

microbiology↗