Biology subjects

Seekatz, A.

Publications and source records attributed to Seekatz, A..

4 recordsLinked to original sources

bioRxiv2025

Host and Microbe Scale Processes Shape Spatial Variation in Aphaenogaster (Hymenoptera: Formicidae) Genetics and Their Microbiota

Like all ecological communities, host-associated (HA) microbiota are shaped by environmental selection and dispersal limitation. However, unlike communities of free-living organisms, communities of HA microbes experience selection and dispersal at two separate scales - the scale of the microbes and the scale of their hosts. Thus, HA microbes must tolerate not only the environment created by their host (microbe-scale environment), but also, the environment in which their host resides (host-scale environment). Likewise, HA microbes can disperse between hosts through either horizontal or vertical transmission (microbe-scale dispersal) but can also disperse between locations through host movement (host-scale dispersal). In this paper, we examine how multiscale environmental selection and dispersal limitation shape the genetics and HA microbiota of ants in the Aphaenogaster fulva-rudis-texana (Hymenoptera: Formicidae) complex. We begin by showing how spatial variation in Aphaenogaster genetics is shaped by host-scale environmental selection and dispersal limitation. We then show how this allows both host- and microbe-scale environmental selection to govern spatial variation in Aphaenogaster microbiota. Finally, we discuss the possibility that microbe-scale dispersal limitation also impacts spatial variation in Aphaenogaster microbiota and that this, in turn, may contribute to spatial variation in Aphaenogaster genetics. Ultimately, our results help to shed light on the myriad of interacting factors governing spatial variation in HA microbiota, including the potential for complex, bidirectional interactions between host- and microbe-scale processes.

ecology↗

bioRxiv2025

Early-Life Poultry-Derived Lactobacilli Drive Microbial Succession and Gut Immune Modulation in Broiler Chickens

Probiotic supplementation supports poultry gut health by modulating microbiome and promoting immune development, yet limited information is known about the effects of early, particularly embryonic, supplementation. In this study, we investigated the effects of administering a lactobacilli cocktail in ovo (embryonic day 18), post-hatch, or both on gut immunity and the succession of the cecal microbiota in broilers over five weeks. 16S rRNA gene-based sequencing of cecal contents revealed a steady increase in Shannon diversity during the first three weeks (PERMANOVA, p < 0.005), with community structure stabilizing by week 3 across all groups. In ovo lactobacilli administration improved early hatch rates and modulated microbial composition during early succession, including reductions in Klebsiella and Enterococcus, and enrichment of Lactobacillus, during the first two weeks (MaAsLin2, q < 0.25). These microbiome shifts were accompanied by a reduced expression of pro-inflammatory cytokines (IFN-{gamma}, IL-1{beta}, and IL-8) in cecal tonsils. These findings highlight the transient yet critical role of early-life probiotic interventions in shaping gut microbial colonization and immune response in broiler chickens. More importantly, a single in ovo lactobacilli dose yielded effects comparable to weekly oral or combined administration.

microbiology↗

bioRxiv2018

Spatial and Temporal Analysis of the Stomach and Small Intestinal Microbiota in Fasted Healthy Humans

Although the microbiota in the proximal gastrointestinal (GI) tract has been implicated in health and disease, much of these microbes remains understudied compared to the distal GI tract. This study characterized the microbiota across multiple proximal GI sites over time in healthy individuals.\n\nAs part of a study of the pharmacokinetics of oral mesalamine administration, healthy, fasted volunteers (N=8; 10 observation periods total) were orally intubated with a four-lumen catheter with multiple aspiration ports. Samples were taken from stomach, duodenal, and multiple jejunal sites, sampling hourly ([≤]7 hours) to measure mesalamine (administered at t=0), pH, and 16S rRNA gene-based composition.\n\nWe observed a predominance of Firmicutes across proximal GI sites, with significant variation compared to stool. The microbiota was more similar within individuals over time than between subjects, with the fecal microbiota being unique from that of the small intestine. The stomach and duodenal microbiota displayed highest intra-individual variability compared to jejunal sites, which were more stable across time. We observed significant correlations in the duodenal microbial composition with changes in pH; linear mixed models identified positive correlations with multiple Streptococcus operational taxonomic units (OTU) and negative correlations with multiple Prevotella and Pasteurellaceae OTUs. Few OTUs correlated with mesalamine concentration.\n\nThe stomach and duodenal microbiota exhibited greater compositional dynamics compared to the jejunum. Short-term fluctuations in the duodenal microbiota was correlated with pH. Given the unique characteristics and dynamics of the proximal GI tract microbiota, it is important to consider these local environments in health and disease states.

microbiology↗

bioRxiv2017

Inter-individual Recovery Of The Microbiota And Metabolome Over Time Following Fecal Microbiota Transplantation In Patients With Recurrent Clostridium difficile Infection

A significant proportion of individuals develop recurrent Clostridium difficile infection (CDI) following initial disease. Fecal microbiota transplantation (FMT), a highly effective treatment method for recurrent CDI, has been demonstrated to induce microbiota recovery, a critical component of disease recovery. However, identification of the specific microbes and their functions that directly impact recovery from CDI remains difficult. We assessed for associations among microbial community members and metabolites in patients with recurrent CDI following treatment with FMT over time to identify groups of bacteria with potential restorative functions. Using 16S rRNA gene-based sequencing, we observed marked similarity of the microbiota between recipients following FMT (n = 6, sampling up to 6 months post-FMT) and their respective donors. Increased levels of the secondary bile acid deoxycholic acid and the short chain fatty acids (SCFAs) butyrate, acetate, and propionate were observed post-FMT. To take into account longitudinal sampling and intra-individual differences, we applied a generalized estimating equation approach to model metabolite concentrations with the presence of specific members of the microbiota. Microbial metabolites that were increased following FMT associated with members classified within the Lachnospiraceae, Ruminococcaceae, and unclassified Clostridiales families. In contrast, members of these taxa were inversely associated with primary bile acids. The longitudinal aspect of this study allowed us to characterize individualized patterns of recovery, revealing variability between and within patients following FMT.\n\nIMPORTANCEClostridium difficile infection (CDI) is an urgent and serious healthcare-associated problem. In recent years, fecal microbiota transplantation (FMT) has been successfully used to treat recurrent CDI, a frequent outcome of disease. While it is apparent that FMT promotes recovery of the microbiota, it is unclear how microbes and their functions promote recovery from disease. This study aimed to identify associations among microbes and metabolites following FMT and to identify critical microbial functions following FMT treatment for recurrent CDI. Overall, recovery of the metabolome was highly dynamic and individualized in all patients, who were all successfully treated. Our results suggest that microbial changes following FMT may be highly specific to the donor-recipient relationship. Further understanding of the host-microbe environments necessary to enable successful transplantation of microbes during FMT could aid development of specific microbial therapeutics for recurrent CDI and other gastrointestinal diseases.

microbiology↗