Highlights • Members of the phylum Proteobacteria have a low abundance in the gut of healthy humans. • We provide an overview of correlations between a bloom of Proteobacteria and a diseased state. • ...We explain driving mechanisms for the uncontrolled expansion of the Proteobacteria population. • Proteobacterial load is suggested as a potential diagnostic criterion for dysbiosis and disease.
Calf diarrhea is associated with enteric infections, and also provokes the overuse of antibiotics. Therefore, proper treatment of diarrhea represents a therapeutic challenge in livestock production ...and public health concerns. Here, we describe the ability of a fecal microbiota transplantation (FMT), to ameliorate diarrhea and restore gut microbial composition in 57 growing calves. We conduct multi-omics analysis of 450 longitudinally collected fecal samples and find that FMT-induced alterations in the gut microbiota (an increase in the family Porphyromonadaceae) and metabolomic profile (a reduction in fecal amino acid concentration) strongly correlate with the remission of diarrhea. During the continuous follow-up study over 24 months, we find that FMT improves the growth performance of the cattle. This first FMT trial in ruminants suggest that FMT is capable of ameliorating diarrhea in pre-weaning calves with alterations in their gut microbiota, and that FMT may have a potential role in the improvement of growth performance.
Hydrophobic sponge structure‐based triboelectric nanogenerators using an inverse opal structured film for sustainable energy harvesting over a wide range of humid atmosphere have been successfully ...demonstrated. The output voltage and current density reach a record value of 130 V and 0.10 mA cm−2, respectively, giving over 10‐fold power enhancement, compared with the flat film‐based triboelectric nanogenerator.
Omics in gut microbiome analysis Whon, Tae Woong; Shin, Na-Ri; Kim, Joon Yong ...
The journal of microbiology,
03/2021, Letnik:
59, Številka:
3
Journal Article
Recenzirano
Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of ...metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.
Recent evidence indicates that the composition of the gut microbiota contributes to the development of metabolic disorders by affecting the physiology and metabolism of the host. Metformin is one of ...the most widely prescribed type 2 diabetes (T2D) therapeutic agents.
To determine whether the antidiabetic effect of metformin is related to alterations of intestinal microbial composition.
C57BL/6 mice, fed either a normal-chow diet or a high-fat diet (HFD), were treated with metformin for 6 weeks. The effect of metformin on the composition of the gut microbiota was assessed by analysing 16S rRNA gene sequences with 454 pyrosequencing. Adipose tissue inflammation was examined by flow cytometric analysis of the immune cells present in visceral adipose tissue (VAT).
Metformin treatment significantly improved the glycaemic profile of HFD-fed mice. HFD-fed mice treated with metformin showed a higher abundance of the mucin-degrading bacterium Akkermansia than HFD-fed control mice. In addition, the number of mucin-producing goblet cells was significantly increased by metformin treatment (p<0.0001). Oral administration of Akkermansia muciniphila to HFD-fed mice without metformin significantly enhanced glucose tolerance and attenuated adipose tissue inflammation by inducing Foxp3 regulatory T cells (Tregs) in the VAT.
Modulation of the gut microbiota (by an increase in the Akkermansia spp. population) may contribute to the antidiabetic effects of metformin, thereby providing a new mechanism for the therapeutic effect of metformin in patients with T2D. This suggests that pharmacological manipulation of the gut microbiota in favour of Akkermansia may be a potential treatment for T2D.
Insects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we ...comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (± 97.7) OTUs per sample. The insect gut microbiota were dominated by Proteobacteria (62.1% of the total reads, including 14.1% Wolbachia sequences) and Firmicutes (20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities.
This paper describes a practical method for obtaining the spectra of lights emitted by a fluor in a liquid scintillator (LS) using a digital camera. The emission wavelength results obtained using a ...digital image were compared with those obtained using a fluorescence spectrophotometer. For general users, conventional spectrophotometers are expensive and difficult to access. Moreover, their experimental measurement setup and processes are highly complicated, and they require considerable care in handling. To overcome these limitations, a feasibility study was performed to obtain the emission spectrum through image analysis. Specifically, the emission spectrum of a fluor dissolved in a liquid scintillator was obtained using digital image analysis. An image processing method was employed to convert the light irradiated during camera exposure into wavelengths. Hue (H) and wavelength (W) are closely related. Thus, we obtained an H-W response curve in the 400~450 nm wavelength region, using a light-emitting diode. Another relevant advantage of the method described in this study is its non-invasiveness in sealed LS samples. Our results showed that this method has the potential to accurately investigate the emission wavelengths of fluor within acceptable uncertainties. We envision the use of this method to perform experiments in chemistry and physics laboratories in the future.
Alterations in the gut microbiota play a crucial role in host physiology and metabolism; however, the molecular pathways underlying these changes in diet-induced obesity are unclear. Mechanistic ...target of rapamycin (mTOR) signaling pathway is associated with metabolic disorders such as obesity and type 2 diabetes (T2D). Therefore, we examined whether changes in the regulation of mTOR signaling induced by diet (a high-fat diet HFD or normal-chow diet) and/or therapeutics (resveratrol a specific inhibitor of mTOR complex 1 or rapamycin an inhibitor of both mTOR complex 1 and 2) altered the composition of the gut microbiota in mice. Oral administration of resveratrol prevented glucose intolerance and fat accumulation in HFD-fed mice, whereas rapamycin significantly impaired glucose tolerance and exacerbated intestinal inflammation. The abundance of Lactococcus, Clostridium XI, Oscillibacter, and Hydrogenoanaerobacterium increased under the HFD condition; however, the abundance of these species declined after resveratrol treatment. Conversely, the abundance of unclassified Marinilabiliaceae and Turicibacter decreased in response to a HFD or rapamycin. Taken together, these results demonstrated that changes in the composition of intestinal microbiota induced by changes in mTOR activity correlate with obese and diabetic phenotypes.
Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous ...microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.
We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).
Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The
gene is controlled by regulatory subunits ...that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50-70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (
) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes,
and
, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the
/
gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the
-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the
gene plays a key role in SI. Finally, self-compatible T-DNA-free T
gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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