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1. Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and faeces

   https://doi.org/10.1111/1755-0998.13573  

   Bunker, Marie E.; Martin, Mark O.; Weiss, Stacey L. (December 2021, Molecular Ecology Resources)

   Abstract Microbial diversity and community function are related, and can be highly specialized in different gut regions. The cloacal microbiome ofSceloporus virgatusfemales provides antifungal protection to eggshells, a specialized function that suggests a specialized microbiome. Here, we describe the cloacal, intestinal, and oviductal microbiome fromS.virgatusgravid females, adding to growing evidence of microbiome localization in reptiles and other taxa. We further assessed whether common methods for sampling gastrointestinal (GI) microbes – cloacal swabs and faeces – provide accurate representations of these microbial communities. We found that different regions of the gut had unique microbial communities. The cloacal microbiome showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83%Enterobacteriacaea(Family).Enterobacteriacaeadecreased up the GI and reproductive tracts. Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues. In contrast, faecal samples had much higher diversity and a distinct composition (common Phyla: 62% Firmicutes, 18% Bacteroidetes, 10% Proteobacteria; common families: 39%Lachnospiraceae, 11%Ruminococcaceae, 11%Bacteroidaceae) relative to all gut regions. The common families in faecal samples made up <1% of cloacal tissue samples, increasing to 43% at the upper intestine. Similarly, the common families in gut tissue (EnterobacteriaceaeandHelicobacteraceae) made up <1% of the faecal microbiome. Further, we found that cloacal swabs taken shortly after defaecation may be contaminated with faecal matter. Our results serve as a caution against using faeces as a proxy for GI microbes, and may help explain high between‐sample variation seen in some studies using cloacal swabs. 

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2. Cloacal microbiomes of sympatric and allopatric Sceloporus lizards vary with environment and host relatedness

   https://doi.org/10.1371/journal.pone.0279288  

   Bunker, Marie E.; Weiss, Stacey L. (December 2022, PLOS ONE)

   Ruiz-Rodriguez, Magdalena (Ed.)

   Animals and their microbiomes exert reciprocal influence; the host’s environment, physiology, and phylogeny can impact the composition of the microbiome, while the microbes present can affect host behavior, health, and fitness. While some microbiomes are highly malleable, specialized microbiomes that provide important functions can be more robust to environmental perturbations. Recent evidence suggests Sceloporus virgatus has one such specialized microbiome, which functions to protect eggs from fungal pathogens during incubation. Here, we examine the cloacal microbiome of three different Sceloporus species (spiny lizards; Family Phrynosomatidae)– Sceloporus virgatus , Sceloporus jarrovii , and Sceloporus occidentalis . We compare two species with different reproductive modes (oviparous vs. viviparous) living in sympatry: S . virgatus and S . jarrovii . We compare sister species living in similar habitats (riparian oak-pine woodlands) but different latitudes: S . virgatus and S . occidentalis . And, we compare three populations of one species ( S . occidentalis ) living in different habitat types: beach, low elevation forest, and the riparian woodland. We found differences in beta diversity metrics between all three comparisons, although those differences were more extreme between animals in different environments, even though those populations were more closely related. Similarly, alpha diversity varied among the S . occidentalis populations and between S . occidentalis and S . virgatus , but not between sympatric S . virgatus and S . jarrovii . Despite these differences, all three species and all three populations of S . occcidentalis had the same dominant taxon, Enterobacteriaceae . The majority of the variation between groups was in low abundance taxa and at the ASV level; these taxa are responsive to habitat differences, geographic distance, and host relatedness. Uncovering what factors influence the composition of wild microbiomes is important to understanding the ecology and evolution of the host animals, and can lead to more detailed exploration of the function of particular microbes and the community as a whole. 

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3. The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus

   https://doi.org/10.1093/femsec/fiae011  

   Bunker, Marie E.; Weiss, Stacey L. (February 2024, FEMS Microbiology Ecology)

   Abstract Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well-studied in humans and other mammals but are less well-understood in egg-laying animals, especially those with no parental care. Here, we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus virgatus. We compared the microbiota of three maternal tissues—oviduct, cloaca, and intestine—to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that maternal identity is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiota in all three sample types, with minimal microbes sourced from maternal intestines. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and the tissue-level variation of the adult S. virgatus microbiota must develop as the hatchling matures. Despite differences between adult and hatchling communities, offspring microbiota were primarily members of the Enterobacteriaceae and Yersiniaceae families (Phylum Proteobacteria), consistent with this and past studies of adult S. virgatus microbiomes. 

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4. Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

   https://doi.org/10.1128/spectrum.01643-21  

   Asangba, Abigail E.; Mugisha, Lawrence; Rukundo, Joshua; Lewis, Rebecca J.; Halajian, Ali; Cortés-Ortiz, Liliana; Junge, Randall E.; Irwin, Mitchell T.; Karlson, Johan; Perkin, Andrew; et al (June 2022, Microbiology Spectrum)

   Kormas, Konstantinos Aristomenis (Ed.)

   ABSTRACT The study of the mammalian microbiome serves as a critical tool for understanding host-microbial diversity and coevolution and the impact of bacterial communities on host health. While studies of specific microbial systems (e.g., in the human gut) have rapidly increased, large knowledge gaps remain, hindering our understanding of the determinants and levels of variation in microbiomes across multiple body sites and host species. Here, we compare microbiome community compositions from eight distinct body sites among 17 phylogenetically diverse species of nonhuman primates (NHPs), representing the largest comparative study of microbial diversity across primate host species and body sites. Analysis of 898 samples predominantly acquired in the wild demonstrated that oral microbiomes were unique in their clustering, with distinctive divergence from all other body site microbiomes. In contrast, all other body site microbiomes clustered principally by host species and differentiated by body site within host species. These results highlight two key findings: (i) the oral microbiome is unique compared to all other body site microbiomes and conserved among diverse nonhuman primates, despite their considerable dietary and phylogenetic differences, and (ii) assessments of the determinants of host-microbial diversity are relative to the level of the comparison (i.e., intra-/inter-body site, -host species, and -individual), emphasizing the need for broader comparative microbial analyses across diverse hosts to further elucidate host-microbial dynamics, evolutionary and biological patterns of variation, and implications for human-microbial coevolution. IMPORTANCE The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution. 

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5. Stable and transient structural variation in lemur vaginal, labial, and axillary microbiomes: Patterns by species, body site, ovarian hormones, and forest access

   https://doi.org/10.1093/femsec/fiaa090  

   Bornbusch, Sally L; Grebe, Nicholas M; Lunn, Siera; Southworth, Chelsea A; Dimac-Stohl, Kristin; Drea, Christine (May 2020, FEMS Microbiology Ecology)

   Abstract Host-associated microbiomes shape and are shaped by myriad processes that ultimately delineate their symbiotic functions. Whereas a host's stable traits, such as its lineage, relate to gross aspects of its microbiome structure, transient factors, such as its varying physiological state, relate to shorter-term, structural variation. Our understanding of these relationships in primates derives principally from anthropoid studies and would benefit from a broader, comparative perspective. We thus examined the vaginal, labial, and axillary microbiota of captive, female ring-tailed lemurs (Lemur catta) and Coquerel's sifakas (Propithecus coquereli), across an ovarian cycle, to better understand their relation to stable (e.g. species identity/mating system, body site) and transient (e.g. ovarian hormone concentration, forest access) host features. We used 16S amplicon sequencing to determine microbial composition and enzyme-linked immunosorbent assays to measure serum hormone concentrations. We found marked variation in microbiota diversity and community composition between lemur species and their body sites. Across both host species, microbial diversity was significantly correlated with ovarian hormone concentrations; negatively with progesterone and positively with estradiol. The hosts’ differential forest access related to the diversity of environmental microbes, particularly in axillary microbiomes. Such transient endogenous and exogenous modulators have potential implications for host reproductive health and behavioral ecology. 

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