Biology subjects

Theis, K. R.

Publications and source records attributed to Theis, K. R..

12 recordsLinked to original sources

bioRxiv2024

Cultivation and molecular characterization of Foley catheterized urine, clean catch urine, and vaginal swabs from pregnant women prior to delivery

The bladder and urine have historically been considered sterile, especially in the context of clinical assessment. Yet, enhanced culture techniques and advances in DNA sequencing surveys have revealed a low microbial biomass microbiota in the bladders of most healthy individuals. Yet very few studies have investigated the urinary microbiota of pregnant women, who are at increased risk of urinary tract infections (UTIs) that can lead to pregnancy complications such as spontaneous preterm birth. To better understand the potential role of a bladder microbiota during pregnancy, we characterized the urinary microbiota of 25 pregnant women (delivering at or beyond 36 weeks gestation) by comparing the bacterial profiles of their paired catheter urine, clean catch urine, and vaginal swabs through both cultivation and molecular microbiological survey methods. For culture, three bacterial taxa were detected in at least 20% of all urine samples (Lactobacillus species, coagulase negative Staphylococcus species, and Ureaplasma urealyticum). All three taxa were detected less frequently in Foley catheter urine than in clean catch urine. Ureaplasma urealyticum was the most frequently recovered bacterium in Foley catheter urine (13/25 women). It was also identified as being more relatively abundant in Foley catheter urine than in the vagina through 16S rRNA gene surveys. Other lower abundance Gram-positive anaerobic cocci (i.e., Finegoldia and Anaerococcus) were also more relatively abundant in Foley catheter urine than clean catch urine or vaginal swabs. However, all sample types had high relative abundances of Lactobacillus and Gardnerella species. Overall, this suggests that, although vaginal microbiota contamination cannot be completely avoided, Foley catheterized urine is effective at characterizing the low abundance bladder microbiota, including Ureaplasma, Finegoldia, and Anaerococcus species. This warrants their further consideration as commensal members of the bladder microbiome during pregnancy.

microbiology↗

bioRxiv2023

M2-polarized macrophages prevent preterm birth and improve neonatal survival and immunity

Preterm birth (PTB), often preceded by preterm labor, is a major cause of neonatal morbidity and mortality worldwide. Most PTB cases involve intra-amniotic inflammation without detectable microorganisms, termed in utero sterile inflammation, for which there is no established treatment. Here, we propose homeostatic macrophages to prevent PTB and adverse neonatal outcomes caused by in utero sterile inflammation. Single-cell atlases of the maternal-fetal interface revealed that homeostatic maternal macrophages are reduced with human labor. M2 macrophage treatment prevented PTB and reduced adverse neonatal outcomes in mice with in utero sterile inflammation. Specifically, M2 macrophages halted premature labor by suppressing inflammatory responses in the amniotic cavity, including inflammasome activation, and mitigated placental and offspring lung inflammation. Moreover, M2 macrophages restored neonatal gut homeostasis and enhanced resistance to systemic bacterial infection. Our findings show that M2 macrophages are a promising strategy to mitigate PTB and improve neonatal outcomes from in utero sterile inflammation.

immunology↗

bioRxiv2023

The vaginal microbiota of pregnant women varies with gestational age, maternal age, and parity

The composition of the vaginal microbiota is heavily influenced by pregnancy and may factor into pregnancy complications, including spontaneous preterm birth. However, results among studies have been inconsistent, due in part to variation in sample sizes and ethnicity. Thus an association between the vaginal microbiota and preterm labor continues to be debated. Yet, before assessing associations between the composition of the vaginal microbiota and preterm labor, a robust and in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required. Herein, we report a large longitudinal study (N = 474 women, 1862 vaginal samples) of a primarily African-American cohort- which experiences a relatively high rate of pregnancy complications - evaluating associations between individual identity, gestational age, and other maternal characteristics with the composition of the vaginal microbiota throughout gestation resulting in term delivery. The primary factors influencing the composition of the vaginal microbiota in pregnancy are individual identity and gestational age at sampling. Secondary factors are maternal age, parity, obesity, and self-reported Cannabis use. The principal pattern across gestation is for the vaginal microbiota to remain or transition to a state of Lactobacillus dominance. This pattern can be mitigated by maternal parity and obesity. Regardless, network analyses reveal dynamic associations among specific bacterial taxa within the vaginal ecosystem, which shift throughout the course of pregnancy. This study provides a robust foundational understanding of the vaginal microbiota in pregnancy among African-Americans, in particular, and sets the stage for further investigation of this microbiota in obstetrical disease. IMPORTANCEThere is debate regarding links between the vaginal microbiota and pregnancy complications, especially spontaneous preterm birth. Inconsistencies in results among studies are likely due to differences in sample sizes and cohort ethnicity. Ethnicity is a complicating factor because, although all bacterial taxa commonly inhabiting the vagina are present among all ethnicities, the frequencies of these taxa vary among ethnicities. Therefore, an in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required prior to evaluating associations between the vaginal microbiota and obstetrical disease. This initial investigation is a large longitudinal study of the vaginal microbiota throughout gestation resulting in a term delivery in a primarily African-American cohort, a population that experiences disproportionally negative maternal-fetal health outcomes. It establishes the magnitude of associations between maternal characteristics, such as age, parity, BMI, and self-reported Cannabis use, on the vaginal microbiota in pregnancy.

microbiology↗

bioRxiv2022

Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study

The gut microbiome provides vital functions for mammalian hosts, yet research on the variability and function of the microbiome across adult lifespans and multiple generations is limited in large mammalian carnivores. Here we use 16S rRNA gene and metagenomic sequencing to profile the taxonomic composition, genomic diversity, and metabolic function of the gut microbiome of 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya over a 23-year period spanning three generations. We determined the extent to which host factors predict variation in the gut microbiome and identify the core microbes present in the guts of hyenas. We also investigate novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition was highly variable across the two decades of sampling, but despite this, a core set of 14 bacterial genera and 19 amplicon sequence variants were identified. The strongest predictors of microbiome alpha and beta-diversity were host identity and age, suggesting that hyenas possess individualized microbiomes, and that these may change with age during adulthood. Gut microbiome functional profiles were also individual-specific, and were moderately correlated with antelope prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyena gut, spanning 25 bacterial orders and 51 genera. Some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species level matches to genomes in existing reference databases. ImportanceThere is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a hosts lifespan and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we demonstrate that although gut microbiomes are individualized and temporally variable among hyenas, they correlate similarly to large-scale changes in their hosts ecological environment. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores but over 80% of MAGs were novel and from species previously not represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of non-model wild hosts, using multiple sequencing methods and computational approaches, and at distinct scales of analysis.

microbiology↗

bioRxiv2022

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets

The existence of a placental microbiota is under debate. The human placenta has historically been considered sterile and microbial colonization has been associated with adverse pregnancy outcomes. Yet, recent investigations using DNA sequencing reported a microbiota in human placentas from typical term pregnancies. However, this detected microbiota could represent background DNA contamination. Using fifteen publicly available 16S rRNA gene datasets, existing data were uniformly re-analyzed. 16S rRNA gene Amplicon Sequence Variants (ASVs) identified as Lactobacillus were highly abundant in eight of fifteen studies. However, the prevalence of Lactobacillus, a typical vaginal bacterium, was clearly driven by bacterial contamination from vaginal delivery and background DNA. After removal of likely DNA contaminants, Lactobacillus ASVs were highly abundant in only one of five studies for which data analysis could be restricted to placentas from term cesarean deliveries. A six study sub-analysis targeting the 16S rRNA gene V4 hypervariable region demonstrated that bacterial profiles of placental samples and technical controls share principal bacterial ASVs and that placental samples clustered primarily by study origin and mode of delivery. Across studies, placentas from typical term pregnancies did not share a consistent bacterial taxonomic signal. Contemporary DNA- based evidence does not support the existence of a placental microbiota. IMPORTANCEEarly-gestational microbial influences on human development are unclear. By applying DNA sequencing technologies to placental tissue, bacterial DNA signals were observed, leading some to conclude that a live bacterial placental microbiome exists in typical term pregnancy. However, the low-biomass nature of the proposed microbiome and high sensitivity of current DNA sequencing technologies indicate that the signal may alternatively derive from environmental or delivery-associated bacterial DNA contamination. Here we address these alternatives with a re- analysis of 16S rRNA gene sequencing data from 15 publicly available placental datasets. After identical DADA2 pipeline processing of the raw data, subanalyses were performed to control for mode of delivery and environmental DNA contamination. Both environment and mode of delivery profoundly influenced the bacterial DNA signal from term-delivered placentas. Aside from these contamination-associated signals, consistency was lacking across studies. Thus, placentas delivered at term are unlikely to be the original source of observed bacterial DNA signals.

microbiology↗

bioRxiv2022

Bacterial profiles of the human placenta from term and preterm deliveries

Whether the human placenta is a sterile organ is under debate. Yet, infection of the amniotic cavity, including the placenta, is causally linked to preterm birth. This study compares the bacterial profiles of term and preterm placentas through culture and 16S rRNA gene sequencing of the amnion, amnion-chorion interface, subchorion, villous tree, and basal plate, while accounting for patient identity, mode of delivery, presence/absence of labor, and potential background DNA contamination. As no evidence of a placental microbiota in term pregnancy was found, these placentas were considered as controls. Placentas from preterm birth cases were more likely to yield bacterial cultures, and their bacterial DNA profiles were less rich than those of term controls, suggesting the predominance of only a few bacteria. Nevertheless, the bacterial DNA profiles of placentas from preterm cases and term controls were not consistently different. The placentas from preterm cases may often have a microbiota but the bacteria constituting these communities varied among the women. Mode of delivery had a pronounced effect on the bacterial profiles of all sampled levels of the placenta. Specifically, the bacterial DNA profiles of vaginally delivered placentas had higher relative abundances of Finegoldia, Gardnerella, Peptoniphilus, and Prevotella (each a common resident of the vaginal microbiota) than the profiles of cesarean-delivered placentas. Collectively, these data indicate that there is a not a placental microbiota in normal term pregnancy, and that although the placentas of some preterm cases were populated by bacteria, the identities of these bacteria varied among women delivering preterm. IMPORTANCEIf a placental microbiota exists, then current understanding of the roles of microorganisms in pregnancy outcomes need to be reconsidered. For instance, we will need to determine if a placental microbiota is beneficial to pregnancy outcome by excluding potential pathogens from colonizing the placenta and/or effectively priming the fetal immune system, and furthermore which characteristics of the placental microbiota preclude versus promote placental infection, which can result in pregnancy complications such as preterm birth. Our findings here are consistent with prior investigations that have reported that there is not a placental microbiota in typical human pregnancies. Yet, bacteria can be detected in placentas from preterm deliveries. The principal source of microorganisms invading the amniotic cavity, including the placenta, is the vaginal microbiota. Focus should be on elucidating the metabolic and/or virulence characteristics of the subset of bacteria within the vaginal microbiota that commonly invade the amniotic cavity, resulting in infection.

microbiology↗

bioRxiv2022

Microbiota of the pregnant mouse: characterization of the bacterial communities in the oral cavity, lung, intestine, and vagina through culture and DNA sequencing

Mice are frequently used as animal models for mechanistic studies of infection and obstetrical disease, yet characterization of the murine microbiota during pregnancy is lacking. The objective of this study was to therefore characterize the microbiotas of distinct body sites of the pregnant mouse that harbor microorganisms that could potentially invade the murine amniotic cavity leading to adverse pregnancy outcomes: vagina, oral cavity, intestine, and lung. The microbiotas of these body sites were characterized through anoxic, hypoxic, and oxic culture, as well as through 16S rRNA gene sequencing. With the exception of the vagina, the cultured microbiotas of each body site varied with atmosphere, with the greatest diversity in the cultured microbiota appearing under anoxic conditions. Only cultures of the vagina were able to recapitulate the microbiota observed from direct DNA sequencing of body site samples, primarily due to the dominance of two Rodentibacter strains. Identified as R. pneumotropicus and R. heylii, these isolates exhibited dominance patterns similar to those of Lactobacillus crispatus and L. iners in the human vagina. Whole genome sequencing of these Rodentibacter strains revealed shared genomic features, including the ability to degrade glycogen, an abundant polysaccharide in the vagina. In summary, we report body site specific microbiotas in the pregnant mouse with potential ecological parallels to those of humans. Importantly, our findings indicate that the vaginal microbiota of pregnant mice can be readily cultured, suggesting that mock vaginal microbiotas can be tractably generated and maintained for experimental manipulation in future mechanistic studies of host vaginal-microbiome interactions. IMPORTANCEMice are widely utilized as animal models of obstetrical complications; however, the characterization of the murine microbiota has been neglected during pregnancy. Microorganisms from the vagina, oral cavity, intestine, and lung have been found in the intra-amniotic space, where their presence threatens the progression of gestation. Herein, we characterize the microbiotas of pregnant mice and establish the appropriateness of culture in capturing the microbiota at each site. The high relative abundance of Rodentibacter observed in the vagina is similar to that of Lactobacillus in humans, suggesting potential ecological parallels. Importantly, we report that the vaginal microbiota of the pregnant mouse can be readily cultured under hypoxic conditions, demonstrating that mock microbial communities can be utilized to test the potential ecological parallels between microbiotas in human and murine pregnancy, and to evaluate the relevance of the structure of these microbiotas for adverse pregnancy outcomes, especially intra-amniotic infection and spontaneous preterm birth.

microbiology↗

bioRxiv2021

LACK OF EVIDENCE FOR A VIABLE MICROBIOTA IN MURINE AMNIOTIC FLUID

The existence of an amniotic fluid microbiota (i.e., a viable microbial community) in mammals is controversial. Its existence would require a fundamental reconsideration of the role of intra-amniotic microbes in fetal development and pregnancy outcomes. In this study, we determined whether the amniotic fluid of mice harbors a microbiota in late gestation. Bacterial profiles of amniotic fluids located proximally or distally to the cervix were characterized through quantitative real-time PCR, 16S rRNA gene sequencing, and culture (N = 21 mice). These profiles were compared to those of technical controls for background DNA contamination. The load of 16S rDNA in the amniotic fluid exceeded that in controls. Additionally, the 16S rDNA profiles of the amniotic fluid differed from those of controls, with Corynebacterium tuberculostearicum being differentially more abundant in amniotic fluid profiles; however, this bacterium was not cultured. Of the 42 total bacterial cultures of amniotic fluids, only one yielded bacterial growth - Lactobacillus murinus. The 16S rRNA gene of this common murine-associated bacterium was not detected in any amniotic fluid sample, suggesting it did not originate from the amniotic fluid. No differences in 16S rDNA load, 16S rDNA profile, or bacterial culture were observed between amniotic fluids located proximal and distal to the cervix. Collectively, these data show that, although there is a modest DNA signal of bacteria in murine amniotic fluid, there is no evidence that this signal represents a viable microbiota. These findings refute the proposed role of amniotic fluid as a source of microorganisms for in utero colonization. IMPORTANCEThe prevailing paradigm in obstetrics has been the sterile womb hypothesis, which posits that fetuses are first colonized by microorganisms during labor and/or the vaginal delivery process. However, it has been suggested that fetuses are consistently colonized in utero. One proposed source of colonizers is the amniotic fluid surrounding the fetus. This concept has been derived primarily from investigations that relied on DNA sequencing. Due to the low microbial biomass of amniotic fluid, such studies are susceptible to influences of background DNA contamination. Additionally, even if there is a microbial DNA signature in amniotic fluid, this is not necessarily reflective of a resident microbiota that could colonize the mammalian fetus. In the current study, using multiple microbiologic approaches and incorporating technical controls for DNA contamination, we show that, although there is a low abundance bacterial DNA signal in amniotic fluid, this does not translate to the presence of viable bacteria.

microbiology↗

bioRxiv2020

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host dietary guild in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders. We found that gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity among gut microbiotas increased with host phylogenetic relatedness (r=0.73), yet this relationship was not consistent among seven closely related Bovid host species (r=0.21 NS). Within bovids, host dietary guild explained more of the variation in the gut microbiota than did host species. Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota, but these gut microbial communities could be furthered modified by host ecology, especially among closely related host species.

ecology↗

bioRxiv2020

Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques

The prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor ([~]130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques. IMPORTANCEMicrobial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.

microbiology↗

bioRxiv2019

No consistent evidence for microbiota in murine placental and fetal tissues

The existence of a placental microbiota and in utero colonization of the fetus has been the subject of recent debate. The objective of this study was to determine whether the placental and fetal tissues of mice harbor bacterial communities. Bacterial profiles of the placenta and fetal brain, lung, liver, and intestine were characterized through culture, qPCR, and 16S rRNA gene sequencing. These profiles were compared to those of the maternal mouth, lung, liver, uterus, cervix, vagina, and intestine, as well as to background technical controls. Positive bacterial cultures from placental and fetal tissues were rare; of the 165 total bacterial cultures of placental tissues from the 11 mice included in this study, only nine yielded at least a single colony, and five of those nine positive cultures came from a single mouse. Cultures of fetal intestinal tissues yielded just a single bacterial isolate: Staphylococcus hominis, a common skin bacterium. Bacterial loads of placental and fetal brain, lung, liver, and intestinal tissues were not higher than those of DNA contamination controls and did not yield substantive 16S rRNA gene sequencing libraries. From all placental or fetal tissues (N = 49), there was only a single bacterial isolate that came from a fetal brain sample having a bacterial load higher than that of contamination controls and that was identified in sequence-based surveys of at least one of its corresponding maternal samples. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of bacterial communities in the placental and fetal tissues of mice. IMPORTANCEThe prevailing paradigm in obstetrics has been the sterile womb hypothesis, which posits that fetuses are first colonized by microorganisms during the delivery process. However, some are now suggesting that fetuses are consistently colonized by microorganisms in utero by microbial communities that inhabit the placenta and intra-amniotic environment. Given the established causal role of microbial invasion of the amniotic cavity (i.e. intra-amniotic infection) in pregnancy complications, especially preterm birth, if the in utero colonization hypothesis were true, there are several aspects of current understanding that will need to be reconsidered including the magnitude of intra-amniotic microbial load required to cause disease and their potential influence on the ontogeny of the immune system. However, acceptance of the in utero colonization hypothesis is premature. Herein, we do not find consistent evidence for placental and fetal microbiota in mice using culture, qPCR, and DNA sequencing.

microbiology↗

bioRxiv2017

Microbial community structure corresponds to nutrient gradients and human impact within coastal wetlands of the Great Lakes.

Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystems services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships between nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa which may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.

microbiology↗