Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota - Microbiome

12/6/2022 7:09:00 PM

A study published in @MicrobiomeJ reports how the social environment and host selection interact to shape the assembly and ontogenesis of the avian gut microbiota. Read the paper here:

A study published in MicrobiomeJ reports how the social environment and host selection interact to shape the assembly and ontogenesis of the avian gut microbiota. Read the paper here:

Background The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social environment and host selection throughout host ontogeny remains understudied, particularly in avian species. We conducted conspecific and heterospecific cross-fostering experiments in zebra finches (Taeniopygia guttata) and Bengalese finches (Lonchura striata domestica) under controlled conditions and repeatedly sampled the faecal microbiota of these birds over the first 3 months of life. We thus documented the development of the gut microbiota and characterised the relative impacts of the early social environment and host selection due to species-specific characteristics and individual genetic backgrounds across ontogeny by using 16S ribosomal RNA gene sequencing. Results The taxonomic composition and community structure of the gut microbiota changed across ontogenetic stages; juvenile zebra finches exhibited higher alpha diversity than adults at the post-breeding stage. Furthermore, in early development, the microbial communities of juveniles raised by conspecific and heterospecific foster parents resembled those of their foster family, emphasising the importance of the social environment. In later stages, the social environment continued to influence the gut microbiota, but host selection increased in importance. Conclusions We provided a baseline description of the developmental succession of gut microbiota in zebra finches and Bengalese finches, which is a necessary first step for understanding the impact of the early gut microbiota on host fitness. Furthermore, for the first time in avian species, we showed that the relative strengths of the two forces that shape the establishment and maintenance of the gut microbiota (i.e. host selection and dispersal from the social environment) change during development, with host selection increasing in import

].By Neha MathurDec 6 2022Reviewed by Danielle Ellis, B.By Senior Trends Reporter, HuffPost UK 05/12/2022 03:12pm GMT.49 ].

Decreases in the microbial similarity between juveniles and their conspecific foster relatives over development We investigated the influence of intraspecific selection mechanisms and social transmission on the establishment of the gut microbiota using two sets of conspecific cross-fostering experiments.In these experiments, we cross-fostered eggs between the nests of unrelated conspecifics in both zebra finches and Bengalese finches.In a recent study published in PLOS ONE, researchers evaluated co-infections in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients.We compared BC dissimilarity between the paired groups of foster and genetic relatives for each experimental group at 5, 10, 35 and 100 dph.We analysed the gut microbiota of 12 ZF juveniles reared by unrelated conspecifics.Background The coronavirus disease 2019 (COVID-19) ruined people's health and lives globally in the past two years.By comparing the dissimilarity between the microbial communities of these juveniles and their genetic and foster relatives, we found that the microbial communities of the juveniles were more similar to those of their foster relatives than to those of their genetic relatives at 5 dph (Wilcoxon rank-sum exact test: p =0.Plates are manually sealed and mixed thoroughly by vortexing and manual shaking, pulsed down briefly, and incubated at room temperature in the dark overnight.

04), 10 dph (Wilcoxon rank-sum exact test: p =0.A meta-analysis reviewed 118 published studies between 2019 and 2021 to find that 19% of COVID-19 patients suffered from co-infections.017) and 35 dph (Wilcoxon rank-sum exact test: p 8 ).At 100 dph, there was no significant difference in the similarity of microbial communities between juveniles reared by unrelated conspecifics and their genetic and foster relatives.These studies primarily used real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assays to detect co-infecting pathogens.The distance between the microbial communities of juveniles and those of their foster relatives increased over time (Kruskal–Wallis rank-sum test, p =0.011), with significant differences between 5 and 100 dph (post hoc Dunn's test, p =0.About the study In the present study, researchers analyzed clinical samples submitted to the California Department of Public Health (CDPH) for SARS-CoV-2 diagnostic testing between February 2020 and July 2020 for the presence of viral, bacterial, and fungal co-infecting pathogens and non-pathogens.The robot removes the ethanol, and the plates are manually placed upside down on a paper towel to drain remaining ethanol.

016), 10 and 100 dph (post hoc Dunn’s test, p =0.048) and 35 and 100 dph (post hoc Dunn’s test, p 8 ).Also, the researchers collected most of these samples after the statewide 'Shelter-in-Place' mandate reduced the circulation of respiratory viral pathogens post-March 2020.In contrast, the distance between the microbial communities of juveniles and their genetic relatives did not change over time.In the groups comparing juveniles and their mothers and juveniles and their siblings, microbial distances did not significantly differ between genetic and foster relatives, with one exception: at 10 dph, zebra finches had a gut microbial composition more similar to their foster siblings than to their genetic siblings (Kruskal–Wallis rank-sum test, p =0.This platform quickly processed up to 96 clinical samples simultaneously.04).Picogreen quantification plates are prepared in triplicate on a Hamilton Microlab STAR robot, where each plate contains a row for the standard curve.

In the groups comparing juveniles and their fathers, we did not detect any difference between the genetic and foster groups at any sampling time.Further, it could detect 117 protozoa and 293 archaebacteria.However, the distance between the microbial communities of juveniles and their foster fathers increased as they developed (Kruskal–Wallis rank-sum test, p =0.033).Finally, they performed bioinformatics and statistical analyses to evaluate the microbial profiles of these samples.Fig.8 Microbial dissimilarity of zebra finch juveniles reared by unrelated conspecifics with their genetic and foster relatives.e.Samples were fractionated into approximately 22 fractions, although the number of fractions recovered by manual SIP typically varies despite identical run conditions.

Violin plots with embedded box plots comparing the distribution of pairwise BC dissimilarities between zebra finch juveniles reared by unrelated conspecifics and their genetic relatives (genetic mother, father and siblings) and foster relatives (foster mother, father and siblings) at 5, 10 and 35 dph.Significance differences between foster and genetic relatives were determined based on Wilcoxon rank-sum tests.The five most abundant bacteria detected by the LLDMA in SARS-CoV-2 positive and negative samples were Streptococcus pyogenes, Streptococcus agalactiae, Prevotella intermedia, Streptococcus pneumoniae, and Mycoplasma testudinis.The significance of the change in distance over time in the foster and genetic groups was determined by the Kruskal–Wallis rank-sum test followed by the post hoc Dunn’s test.Significance is highlighted for p.A meta-analysis by Lansbury et al.

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Co-infecting pathogens and the microbiome from SARS-CoV-2 positive and negative samplesCo-infecting pathogens and the microbiome from SARS-CoV-2 positive and negative samples PLOSONE jgi pathogen microbiome SARSCoV2 COVID19 coronavirus covid

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HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi - MicrobiomeBackground Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance—the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. Results Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10–33 atom% 13C), even though the soils’ overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobio

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