Figure - available from: Frontiers in Ecology and Evolution
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Clustered-bar charts (A) depicting phyla level (top 10) variation in gut microbiota composition across sample age based on OTUs and (B) depicting phyla level (top 10) variation in gut microbiota composition across sample age based on ASVs.
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Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse...
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Background:
COVID-19, the disease caused by the highly infectious and transmissible coronavirus SARS-CoV-2, has quickly become a morbid global pandemic. Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children, and adolescents in a standardized manner during th...
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... Methods from DNA extraction through sequencing and analysis followed similar, previously published works by Greiman et al. (2020) [22]. Sample swabs (skin, gill, cloaca, and gut) were DNA extracted using the ZR Fecal DNA MiniPrep TM kit (Zymo Research, Irvine, CA, USA) following the manufacturer's instructions. ...
... The positive control (herein referred to as a mock community) used was ZymoBIOMICS Microbial Community Standard II (Zymo Research, Irvine, CA, USA) and the negative controls included a water blank library amplified in triplicate. PCR amplification and library preparation were carried out following the protocol outlined by Greiman et al. (2020) [22]. Libraries were sequenced on an Illumina MiSeq (paired-end reads; 2 × 250 bp with two 8 bp index reads; 15% PhiX) at the University of Georgia Genomics and Bioinformatics Core (GGBC, UG Athens, GA, USA, RRID:SCR_010994). ...
Comparing co-occurring species may provide insights into how aspects of ecology may play a role in influencing their microbial communities. During the 2019 commercial shrimp trawl season off coastal Georgia, swabs of skin, gills, cloaca, and gut were taken for three species of batoids (Butterfly Ray, Bluntnose Stingray, and Atlantic Stingray) and one shark species (Atlantic Sharpnose) for high-throughput sequencing of the V4 region of the bacterial 16S rRNA gene. White muscle was analyzed for stable isotopes (δ13C and δ15N) to evaluate potential niche overlap in these four sympatric mesopredators. Significant differences were found in both δ13C and δ15N signatures across species, suggesting a degree of resource partitioning. When examined within tissue type, the host species had a weak effect on β-diversity for cloaca and skin, with no differences found for gill and gut samples. However, network analysis metrics demonstrated a stronger species-specific effect and distinct microbial community relationships were apparent between the shark and batoids, with the former having tighter networks for both internally- and externally-influenced tissues (gut/cloaca and skin/gills, respectively). Despite overlapping habitat use, species’ microbiomes differed in their organizational structuring that paralleled differences in stable isotope results, suggesting a mediating role of species-specific ecology on bacterial microbiomes.
... Regarding the age of the samples and the fixation procedure there has been documented contrasting results in other zoological groups. For example, lower diversity values at phyla level and the lack of recovery of less abundant groups has been documented [34,35], but in other works, diversity values maintain stable and the changes in microbiome are explained by the turnover of low abundance phyla [36] Meanwhile, in fishes, a recent published work that compares different storage methods found that ethanol preserved samples outperforms other methods such as immediate freezing, RNA later or nucleic acids shield in DNA quantity, quality, cost and labor [37]. ...
The use of museum preserved specimens to know microbiome in extinct and threatened species has been explored recently. The fishes of the genus Herichthys are distributed mainly in the Pánuco-Tamesí system in Northeastern Mexico, one of the most polluted basins in the country leading to near half of the species be considering as threatened. In this paper we used the hypervariable V4 region of the 16S rRNA gene from the 11 species of the genus Herichthys obtained from museum collections to evaluate the potential use of fixed preserved vouchers in the knowledge of gut microbiota diversity and the potential role of sympatric and allopatric speciation of the hosts in the gut microbiome evolution. The 100% of the samples were successfully amplified where the number of amplicons ranged from 4500 from a formaldehyde fixed specimen up to 55,000 in ethanol preserved specimens. Differences in gut microbiota were found between sympatric species and among the comparison of some trophic guilds. A non-random association between the gut host and their microbiome was found allow to suggest a potential phylosymbiosis relationship. In conclusion, the most abundant phyla recovered from the gut microbiota in this study were similar to those previously reported in other cichlids supporting the idea that a gut microbial core is conserved in this group of fishes despite millions of years of evolution and leading to support the potential use of museum specimens in microbiome studies.
Faunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.
The technological ability to characterize genetic variation at a genome‐wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short‐ to long‐read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long‐read sequencing has tremendous potential but sequencing success strongly depends on the long‐range integrity of DNA molecules and therefore on the availability of high‐quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high‐quality samples may soon be a major concern for many projects. The need for high‐quality biodiversity tissue archives is therefore urgent but sampling and preserving high‐quality samples is not a trivial exercise. In this review, I will briefly outline how long‐read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high‐quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high‐quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long‐term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.
