scholarly journals The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10271 ◽  
Author(s):  
Yan-Fu Qu ◽  
Yan-Qing Wu ◽  
Yu-Tian Zhao ◽  
Long-Hui Lin ◽  
Yu Du ◽  
...  
Keyword(s):  
Information Processing ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Supporting Evidence ◽  
Turtle Species ◽  
Functional Roles ◽  
Pond Turtle ◽  
Mutualistic Symbiosis ◽  
Slider Turtle ◽  
Genetic Information Processing

Background The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. Methods We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. Results The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.

scholarly journals Flavor compounds in fermented Chinese alcoholic beverage alter gut microbiota and attenuate ethanol-induced liver damages

2018 ◽  
Author(s):  
Cheng Fang ◽  
Hai Du ◽  
Zheng Xiaojiao ◽  
Aihua Zhao ◽  
Wei Jia ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Small Molecule ◽  
Relative Abundance ◽  
Alcoholic Beverage ◽  
Intestinal Barrier ◽  
Alcoholic Beverages ◽  
Supporting Evidence ◽  
Pure Ethanol ◽  
Ethanol Feeding ◽  
Fermented Grains

AbstractAlcoholic beverages which are consumed widely in most parts of the world have long been identified as a major risk factor for all liver diseases, particularly alcohol-induced liver disease (ALD). Recent compositional analyses suggest that Chinese Baijiu (CB), a clear alcoholic liquid distilled from fermented grains, contains large amounts of small molecule bioactive compounds in addition to a significant amount of ethanol. Here, in an experimental mouse model, we show that CB caused lower degrees of liver injury than pure ethanol by protecting against the decrease of the relative abundance of Akkermansia and increased relative abundance of Prevotella in the gut thereby preventing the destruction of the intestinal barrier. Furthermore, we demonstrated that ethanol-induced alteration of the gut microbiota profoundly affected the host metabolome. Compared with ethanol feeding, CB feeding resulted in higher concentrations of functional saturated LCFAs and SCFAs. Our results provide supporting evidence that ALD was profoundly influenced by host-gut microbiota metabolic interactions and that small molecule organic compounds in CB could attenuate ALD.

scholarly journals Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota

2019 ◽  
Vol 7 (11) ◽  
pp. 535 ◽  
Author(s):  
Gabriele Andrea Lugli ◽  
Sabrina Duranti ◽  
Christian Milani ◽  
Leonardo Mancabelli ◽  
Francesca Turroni ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Life Span ◽  
Relative Abundance ◽  
Intestinal Mucosa ◽  
Environmental Samples ◽  
Enrichment Method ◽  
Functional Roles ◽  
Genetic Features ◽  
Uptake Of Nutrients

Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa.

scholarly journals Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Xi Chen ◽  
Limin Fan ◽  
Liping Qiu ◽  
Xinxu Dong ◽  
Qing Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Procambarus Clarkii ◽  
Rice Paddy ◽  
Taxonomic Composition ◽  
Glycoside Hydrolases ◽  
Red Swamp Crayfish ◽  
Aquaculture Ponds ◽  
Genetic Information Processing ◽  
And Function

The structure and function of intestinal microorganisms are closely related to host metabolism, development, physiology, and health. The red swamp crayfish, Procambarus clarkii, is an important farmed aquatic species in China, which is grown in aquaculture ponds and rice paddy fields. Since these are two distinct cultivation environments with important differences in nutrient input and ecological community composition, we hypothesized that they may have different effects on the gut microbiota of the crayfish. Here, we sought to examine this hypothesis. To that aim, metagenomics analyses were applied to unveil the taxonomic composition and functional diversity of the microbiota in the intestines of red swamp crayfish grown in aquaculture ponds and rice-crayfish cultivation environments. The results showed that Firmicutes and Proteobacteria were the two most abundant microbial components. In addition, the relative abundance of bacterial and archaeal communities, but not that of fungal and viral communities, significantly differed between the two environments. The abundance of genes involved in pathways related to genetic information processing and human diseases was lower in the guts of red swamp crayfish grown in rice-crayfish cultivation environments. In particular, the abundance of two gene sets, K13730 and K08303, which are related to epithelial cell invasion by Listeria monocytogenes and Helicobacter pylori, respectively, decreased in this culture environment. In addition, the samples from rice-crayfish cultivation environments tended to have lower relative abundance of glycosyltransferases (GTs), which were the most abundant carbohydrate-active enzymes in the samples from both groups, higher abundance of glycoside hydrolases, and lower abundance of GT2.

Does a Ribosome Really Read? On the Cognitive Roots and Heuristic Value of Linguistic Metaphors in Molecular Genetics. Part 2

2020 ◽  
Vol 63 (2) ◽  
pp. 46-62
Author(s):  
Suren T. Zolyan
Keyword(s):  
Information Processing ◽  
Genetic Information ◽  
Formal Organization ◽  
Dual Nature ◽  
Reading Frame ◽  
The Core ◽  
Genetic Information Processing ◽  
Cognitive Frame ◽  
Effective Instrument

We discuss the role of linguistic metaphors as a cognitive frame for the understanding of genetic information processing. The essential similarity between language and genetic information processing has been recognized since the very beginning, and many prominent scholars have noted the possibility of considering genes and genomes as texts or languages. Most of the core terms in molecular biology are based on linguistic metaphors. The processing of genetic information is understood as some operations on text – writing, reading and editing and their specification (encoding/decoding, proofreading, transcription, translation, reading frame). The concept of gene reading can be traced from the archaic idea of the equation of Life and Nature with the Book. Thus, the genetics itself can be metaphorically represented as some operations on text (deciphering, understanding, code-breaking, transcribing, editing, etc.), which are performed by scientists. At the same time linguistic metaphors portrayed gene entities also as having the ability of reading. In the case of such “bio-reading” some essential features similar to the processes of human reading can be revealed: this is an ability to identify the biochemical sequences based on their function in an abstract system and distinguish between type and its contextual tokens of the same type. Metaphors seem to be an effective instrument for representation, as they make possible a two-dimensional description: biochemical by its experimental empirical results and textual based on the cognitive models of comprehension. In addition to their heuristic value, linguistic metaphors are based on the essential characteristics of genetic information derived from its dual nature: biochemical by its substance, textual (or quasi-textual) by its formal organization. It can be concluded that linguistic metaphors denoting biochemical objects and processes seem to be a method of description and explanation of these heterogeneous properties.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Gut microbiota markers associated with obesity and overweight in Italian adults

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Vanessa Palmas ◽  
Silvia Pisanu ◽  
Veronica Madau ◽  
Emanuela Casula ◽  
Andrea Deledda ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Smoking Status ◽  
16S Rrna Gene Sequencing ◽  
Normal Weight ◽  
Activity Level ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Obesity And Overweight ◽  
Rrna Gene Sequencing

AbstractIn the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.

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