Biology subjects

Altshuler, I.

Publications and source records attributed to Altshuler, I..

4 recordsLinked to original sources

bioRxiv2026

Impact of WaSH and dietary practices on age-driven gut microbiome in stunted young children

BackgroundStunting, defined as height-for-age below -2 standard deviations of the WHO child growth standards median, is influenced by nutritional and environmental factors. It remains a public health challenge in Tanzania, particularly in Iringa (prevalence 57%, exceeding the national average of 30%), despite abundant food production. This study explored the gut bacteriome as a potential biomarker for child growth and its association with water, sanitation, and hygiene (WaSH) practices in food-secure settings. MethodsA community-based cross-sectional study (September-October 2024) enrolled children aged 5-23 months in Iringa, collecting fecal samples and household data on growth metrics, WaSH, feeding practices, and illness. The V3-V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq and analysed with QIIME2 and R for alpha and beta diversity, differential abundance (ANCOM-BC), and random forest (RF) modelling. ResultsOverall, 60.5% of 297 children were stunted. Stunting was associated with older age, male gender, discontinued breastfeeding, poor feeding diversity, toilet sharing, and residence location (p < 0.001, p = 0.049, p = 0.001, p = 0.001, p = 0.001, and p = 0.005, respectively). Significant differences in bacterial community composition were observed between stunted and normally growing children (Shannon p = 0.0053; Bray-Curtis p = 0.001). A shared core bacteriome was identified in both groups, influenced by environmental and dietary factors. Normally growing children were enriched with Bifidobacterium, Rothia, Olsenella, Slackia, Lactobacillus, Gemella, and Oscillibacter, while stunted children showed enrichment of Prevotella, Akkermansia, Fusobacterium, Acinetobacter, Alistipes, Odoribacter, Fournierella, and the Ruminococcus torques group. ConclusionAge was the most consistent predictor of gut microbial diversity. Stunting does not appear to be caused by a completely different gut microbiome; instead, shared environmental and dietary factors shape both gut bacteria and child growth. Promoting diverse complementary feeding, continued breastfeeding, and improved hygiene could mitigate risks and inform targeted interventions in food-secure regions.

microbiology↗

bioRxiv2025

Global distribution of microbial carrageenan foraging pathways reveals widespread latent traits within the genetic dark matter of ruminant intestinal microbiomes

Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we applied functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the distal gut over the rumen, and bacterial isolates had capacity to use carrageenans as a sole carbon source. Carrageenan-active polysaccharide utilization loci (CarPULs) were identified and recombinant enzymes were characterized to provide insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining revealed that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a globally distributed latent trait within the order Ruminantia and carried within microbiome as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.

microbiology↗

bioRxiv2024

Protozoal populations drive system-wide variation in the rumen microbiome

While rapid progress has been made to characterize the bacterial and archaeal populations of the rumen microbiome, insight into how they interact with keystone protozoal species remains elusive. Here, we reveal two distinct rumen community types (RCT-A and RCT-B) that are not strongly associated with host phenotype nor genotype but instead linked to protozoal community patterns. We leveraged a series of multi-omic datasets to show that the dominant Epidinium spp. in animals with RCT-B employ a plethora of fiber-degrading enzymes that present enriched Prevotella spp. a favorable carbon landscape to forage upon. Conversely, animals with RCT-A, dominated by genera Isotricha and Entodinium, harbor a more even distribution of fiber, protein, and amino acid metabolizers, reflected by higher detection of metabolites from both protozoal and bacterial activity. We reveal microbiome variation across key protozoal and bacterial populations is interlinked, which should act as an important consideration for future development of microbiome-based technologies.

microbiology↗

bioRxiv2022

The metabolic influence of the core ciliate Entodinium caudatum within the rumen microbiome

Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.

microbiology↗