Biology subjects

Schmitz-Esser, S.

Publications and source records attributed to Schmitz-Esser, S..

9 recordsLinked to original sources

bioRxiv2026

Identification of cytoplasmic incompatibility effectors of the reproductive manipulator Cardinium hertigii

Cytoplasmic incompatibility (CI), a widespread symbiont-induced reproductive manipulation phenotype in arthropods, selectively kills embryonic offspring produced when infected males mate with uninfected females. Most knowledge on CI comes from studying the Pseudomonadota symbiont Wolbachia and their CI effector (cif) genes, and little is known about CI mechanisms of symbionts without cif genes. We identify two putative CI effectors of Cardinium hertigii cEper1, a Bacteroidota symbiont of the parasitoid wasp Encarsia suzannae, using a combined proteomics and heterologous expression approach. We show that these genes, CAHE_0406 and CAHE_p0043, have no homology to known cif genes, yet impair yeast growth similar to known cifs and that CAHE_p0043 localizes to diffuse and fragmented yeast nuclei. These results suggest that CAHE_0406 and/or CAHE_p0043 could play a role in cEper1-induced CI, expanding our current understanding of the diversity of proteins involved in cytoplasmic incompatibility across symbiont lineages.

microbiology↗

bioRxiv2024

Effect of Genotype and Age on a Defined Microbiota in Gnotobiotic SCID Piglets

Severe combined immunodeficient (SCID) individuals lack functional T and B lymphocytes, leading to a deficient adaptive immune system. SCID pigs are a unique large animal biomedical model as they possess many similarities to humans, allowing for the collection of translatable data in regenerative medicine, cancer, and other biomedical research topics. While many studies suggest early gut microbiota development is necessary for developing the intestinal barrier and immune system, these animals are often cesarian section derived, leaving them uncolonized for normal intestinal microflora. The hypothesis was that an increase in complexity of microbiota inoculum will allow for more stability in the composition of the gut microbiota of SCID piglets. This was tested across multiple litters of SCID piglets with three different defined microbiota consortium (2-strain, 6-strain, 7-strain). All piglets received their designated defined microbiota by oral gavage immediately after birth and again 24 hours later. There was no effect of SCID genotype on the composition of the gut microbiota, but there was a significant effect due to piglet age. Additionally, all three defined microbiota consortia were deemed safe to use in SCID piglets, and the 7-strain microbiota was the most stable over time. Based on these results, the 7-strain defined microbiota will be added to the SCID pig husbandry protocol, allowing for a more reproducible model.

genetics↗

bioRxiv2022

Fluorescence In Situ Hybridization Provides Evidence for the Presence of the Endosymbiotic Bacterial Genus Rickettsia in Tardigrades

Many ecdysozoans harbor endosymbiotic bacteria within their microbiota, and these endosymbionts can have a range of positive and negative effects on their hosts. Recent 16S rRNA gene amplicon sequencing studies have provided evidence for endosymbionts within the tardigrade microbiota. In a previous study amplicon study, we determined that sequences corresponding to the endosymbiotic genus Rickettsia were significantly more associated with tardigrades than with the substrate from which they were isolated. Here, we performed fluorescence in situ hybridization (FISH) using a Rickettsia-specific probe, RickB1, to determine if Rickettsia could be found in tardigrades. RickB1 and a probe targeting most bacteria, EUB338, colocalized within the tissues of tardigrades, indicating the presence of Rickettsia. We also performed FISH using RickB1 and a nonsense probe which allowed us to distinguish between false positives and true positives. This method revealed RickB1 signals in tardigrades that were not due to erroneous probe binding, providing further evidence that Rickettsia is present in tardigrades. Future research will be necessary to determine the effects, if any, of this endosymbiont on its tardigrade host.

microbiology↗

bioRxiv2022

Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii

Minute parasitoid wasps in the genus Encarsia are commonly used as biological pest control agents of whiteflies and armored scale insects in greenhouses or in the field. They are also a key host of the bacterial endosymbiont Cardinium hertigii which can cause a suite of reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility; the last being most thoroughly studied in Encarsia suzannae. Despite their biological and economic importance, there are currently no published Encarsia genomes and only one public transcriptome. In this study, we applied a mapping-and-removal approach to eliminate known contaminants from previously-obtained Illumina sequencing data. We generated de novo transcriptome assemblies for both female and male E. suzannae which contain 45,986 and 54,762 final coding sequences, respectively. Benchmarking Single-Copy Orthologs (BUSCO) results indicate both assemblies are highly complete. Preliminary analyses revealed the presence of homologs of sex-determination genes characterized in other insects and putative venom proteins. These transcriptomes will be valuable tools to better understand the biology of Encarsia wasps and their evolutionary relatives. Furthermore, the separate male and female assemblies will be particularly useful references for studies involving insects of only one sex.

genomics↗

bioRxiv2022

Tardigrade community microbiomes in North American orchards include putative endosymbionts and plant pathogens

The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, USA, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades versus their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.

microbiology↗

bioRxiv2020

Influence of the artificial sodium saccharin sweetener Sucram(R) on the microbial community composition in the rumen content and attached to the rumen epithelium in dairy cattle: A pilot study

The products of rumen microbial fermentations are considered essential for animal growth and performance. Changes in these microbial communities can have major effects on animal growth and performance. Saccharin-based artificial sweeteners can be included in livestock diets to increase palatability and encourage feed intake. Despite the importance of the rumen microbial fermentation, little or no research is available regarding how saccharin-based artificial sweeteners affect rumen content and rumen epithelial microbial communities. The aim of this study was to identify changes in both the rumen content and rumen epithelial microbial communities in response to the supplementation of Sucram(R), a sodium-saccharin-based sweetener (Pancosma S.A./ADM Groups, Rolle, Switzerland) during standard, non-stress conditions using 16SrRNA gene amplicon sequencing. The rumen epithelial and rumen content microbiota of five Holstein-Friesian milking dairy cattle were compared before (baseline, BL) and after a 28-day supplementation of Sucram(R). Illumina MiSeq-based 16S rRNA gene sequencing was conducted, and community analysis revealed significant changes in the abundance of specific phylotypes when comparing BL to Sucram(R) experimental groups. Sucram(R) did not have a significant effect on overall rumen microbial community structure between experimental groups. Statistically significant changes in microbial community composition following Sucram(R) supplementation were observed most consistently across a number of bacterial taxa in the rumen epithelium, while fewer changes were seen in the rumen content. Predicted genomic potentials of several significantly different OTUs were mined for genes related to feed efficiency and saccharin degradation. Operational taxonomic units (OTUs) classified as Prevotella and Sharpea were significantly (p<0.05) increased in samples supplemented with Sucram(R), whereas a reduction in abundance was seen for OTUs classified as Treponema, Leptospiraceae, Ruminococcus and methanogenic archaea. This is the first study to report an effect of Sucram(R) on ruminant microbial communities, suggesting possible beneficial impacts of Sucram(R) on animal health and performance that may extend beyond increasing feed palatability.

microbiology↗

bioRxiv2020

The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes

The survival of Listeria (L.) monocytogenes in foods and food production environments (FPE) is dependent on several genes that increase tolerance to stressors; this includes competing with intrinsic bacteria. We aimed to uncover genes that are differentially expressed (DE) in L. monocytogenes sequence type (ST) 121 strain 6179 when co-cultured with cheese rind bacteria. L. monocytogenes was cultivated in broth or on plates with either a Psychrobacter or Brevibacterium isolate from cheese rinds. RNA was extracted from co-cultures in broth after two or 12 hours and from plates after 24 and 72 hours. Broth co-cultivations with Brevibacterium or Psychrobacter yielded up to 392 and 601 DE genes, while plate co-cultivations significantly affected the expression of up to 190 and 485 L. monocytogenes genes, respectively. Notably, the transcription of virulence genes encoding the Listeria adhesion protein and Listeriolysin O were induced during plate and broth co-cultivations. The expression of several systems under the control of the global stress gene regulator, {sigma}B, increased during co-cultivation. A cobalamin-dependent gene cluster, responsible for the catabolism of ethanolamine and 1,2-propanediol, was upregulated in both broth and plate co-cultures conditions. Finally, a small non-coding (nc)RNA, Rli47, was induced after 72 hours of co-cultivation on plates and accounted for 50-90% of the total reads mapped to L. monocytogenes. A recent study has shown that Rli47 may contribute to L. monocytogenes stress survival by slowing growth during stress conditions through the suppression of branch-chained amino acid biosynthesis. We hypothesize that Rli47 may have an impactful role in the response of L. monocytogenes to co-cultivation by regulating a complex network of metabolic and virulence mechanisms.

microbiology↗

bioRxiv2020

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota

Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungus Epichloe coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance groups according to their growth performance (weight gain). 20 HT and 20 LT cattle balanced by farm were selected for 16S rRNA gene and ITS1 region Illumina MiSeq amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (P<0.05) different bacterial and fungal microbiota between HT and LT cattle, and indicates that fungal phylotypes may be important for an animals response to fescue toxicosis: We found that fungal phylotypes affiliating to the Neocallimastigaceae, which are known to be important fiber-degrading fungi, were consistently more abundant in the HT cattle. Whereas fungal phylotypes related to the genus Thelebolus were more abundant in the LT cattle. This study also found more pronounced shifts in the microbiota in animals receiving higher amounts of the toxin. We identified fungal phylotypes which were consistently more abundant either in HT or LT cattle and may thus be associated with the respective animals response to fescue toxicosis. Our results thus suggest that some fungal phylotypes might be involved in mitigating fescue toxicosis. The results of our study provide a basis for investigating the functional role of the gastrointestinal microbiota in fescue toxicosis in more detail in the future.

microbiology↗

bioRxiv2019

A prospective role for the rumen in generating antibiotic resistance

Antibiotics were a revolutionary discovery of the 20th century, but the ability of bacteria to spread the genetic determinants of resistance via horizontal gene transfer (HGT) has quickly endangered their use1. Indeed, there is a global network of microbial gene exchange, the analysis of which has revealed particularly frequent transfer of resistance determinants between farm animals and human-associated bacteria2. Here, we leverage the recent release of a rumen microbial genome reference set and show that the wide-spread resistance gene cluster aadE-sat4-aphA-3 is harboured in ruminal Bacteroidetes. While this cluster appears to have been recently transferred between commensal bacteria in the rumen and many diverse animal and human pathogens, comparative analysis suggests that the cluster stabilized in the pathogens. Then, focusing on streptomycin resistance, it was found that homologues from the rumen span much of the known diversity of aminoglycoside O-nucleotidyltransferases (AadEs) and that distinct variants of the enzyme are present in a single rumen bacterial genome. Notably, a second variant of AadE has also been recently transferred, albeit more often as a single gene, throughout a different set of animal and human associated bacteria. By examining the synteny of AadE orthologues in various bacterial genomes and analyzing corresponding gene trees in an environmental context, we speculate that the ruminant associated microbiome has a salient role in the emergence of specific resistance variants and clusters. In light of the recent literature on the evolutionary origin of antibiotic resistance, we further suggest that the rumen provides a possible route of dissemination of resistance genes from soil resistomes, throughout the farm, and to human pathogens3.

microbiology↗