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.

scholarly journals Mucosal glycan degradation of the host by the gut microbiota

Glycobiology ◽  
2020 ◽  
Author(s):  
Andrew Bell ◽  
Nathalie Juge
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Binding Sites ◽  
Short Review ◽  
Commensal Bacteria ◽  
Glycoside Hydrolases ◽  
Safe Distance ◽  
Human Gut ◽  
And Function

Abstract The gut microbiota plays a major role in human health and an alteration in gut microbiota structure and function has been implicated in several diseases. In the colon, mucus covering the epithelium is critical to maintain a homeostatic relationship with the gut microbiota by harboring a microbial community at safe distance from the epithelium surface. The mucin glycans composing the mucus layer provide binding sites and a sustainable source of nutrients to the bacteria inhabiting the mucus niche. Access to these glycan chains requires a complement of glycoside hydrolases (GHs) produced by bacteria across the phyla constituting the human gut microbiota. Due to the increased recognition of the role of mucus-associated microbes in human health, how commensal bacteria breakdown and utilize host mucin glycans has become of increased interest and is reviewed here. This short review provides an overview of the strategies evolved by gut commensal bacteria to access this rich source of the nutrient with a focus on the GHs involved in mucin degradation.

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 Seasonal Changes in the Distinct Taxonomy and Function of the Gut Microbiota in the Wild Ground Squirrel (Spermophilus dauricus)

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2685
Author(s):  
Xiaoying Yang ◽  
Yuchen Yao ◽  
Xueying Zhang ◽  
Jiahui Zhong ◽  
Fuli Gao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Breeding Season ◽  
Relative Abundance ◽  
Ground Squirrel ◽  
Microbial Community Composition ◽  
Nucleotide Metabolism ◽  
Rrna Gene ◽  
Seasonal Breeding ◽  
And Function ◽  
Breeding Seasons

Seasonal breeding is a normal phenomenon in which animals adapt to natural selection and reproduce only in specific seasons. Large studies have reported that the gut microbiota is closely related to reproduction. The purpose of this study was to explore the distinct taxonomy and function of the gut microbiota in the breeding and non-breeding seasons of the wild ground squirrel (Spermophilus dauricus). The 16S rRNA gene sequencing technology was utilized to sequence the gut microbiota of the wild ground squirrel. PICRUSt analysis was also applied to predict the function of the gut microbiota. The results suggested that the main components of the gut microbiota in all samples were Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between the breeding and non-breeding seasons. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were more abundant in the non-breeding season, while Blautia and Streptococcus were more abundant in the breeding season. The results of a functional prediction suggested that the relative abundance of functional categories that were related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism increased in the breeding season. The relative abundance of energy metabolism, transcription, and signal transduction increased in the non-breeding season. Overall, this study found differences in the taxonomy and function of the gut microbiota of the wild ground squirrel between the breeding and non-breeding seasons, and laid the foundation for further studies on the relationship between the gut microbiota and seasonal breeding.

scholarly journals Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer

2021 ◽  
Vol 12 ◽  
Author(s):  
Feng Jiang ◽  
Hongmei Gao ◽  
Wen Qin ◽  
Pengfei Song ◽  
Haijing Wang ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Captive Breeding ◽  
Cold Season ◽  
Structure And Function ◽  
Musk Deer ◽  
Seasonal Differences ◽  
Metabolic Functions ◽  
And Function

Musk deer (Moschus spp.) is a globally endangered species due to excessive hunting and habitat fragmentation. Captive breeding of musk deer can efficiently relieve the hunting pressure and contribute to the conservation of the wild population and musk supply. However, its effect on the gut microbiota of musk deer is unclear. Recent studies have indicated that gut microbiota is associated with host health and its environmental adaption, influenced by many factors. Herein, high-throughput sequencing of the 16S rRNA gene was used based on 262 fecal samples from forest musk deer (M. berezovskii) (FMD) and 90 samples from alpine musk deer (M. chrysogaster) (AMD). We sought to determine whether seasonal variation can affect the structure and function of gut microbiota in musk deer. The results demonstrated that FMD and AMD had higher α-diversity of gut microbiota in the cold season than in the warm season, suggesting that season change can affect gut microbiota diversity in musk deer. Principal coordinate analysis (PCoA) also revealed significant seasonal differences in the structure and function of gut microbiota in AMD and FMD. Particularly, phyla Firmicutes and Bacteroidetes significantly dominated the 352 fecal samples from captive FMD and AMD. The relative abundance of Firmicutes and the ratio of Firmicutes to Bacteroidetes were significantly decreased in summer than in spring and substantially increased in winter than in summer. In contrast, the relative abundance of Bacteroidetes showed opposite results. Furthermore, dominant bacterial genera and main metabolic functions of gut microbiota in musk deer showed significant seasonal differences. Overall, the abundance of main gut microbiota metabolic functions in FMD was significantly higher in the cold season. WGCNA analysis indicated that OTU6606, OTU5027, OTU7522, and OTU3787 were at the core of the network and significantly related with the seasonal variation. These results indicated that the structure and function in the gut microbiota of captive musk deer vary with seasons, which is beneficial to the environmental adaptation and the digestion and metabolism of food. This study provides valuable insights into the healthy captive breeding of musk deer and future reintroduction programs to recover wild populations.

scholarly journals Two Isomers of Ginger Root Extracts Modify Composition and Function of Gut Microbiota in Rats Treated with Neuropathic Pain

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 394-394
Author(s):  
Moamen Elmassry ◽  
Rui Wang ◽  
Abdul Hamood ◽  
Volker Neugebauer ◽  
Chwan-Li Shen
Keyword(s):  
Neuropathic Pain ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Pentose Phosphate ◽  
Control Group ◽  
Rrna Gene ◽  
Root Extract ◽  
Sprague Dawley ◽  
Fecal Samples ◽  
And Function

Abstract Objectives Emerging evidence has suggested that gut microbiota plays a key role during the development of chronic pain, such as neuropathic pain (NP). This study was to evaluate the effects of two ginger root extract isomers (gingerols and shogaols) on the composition and function of gut microbiota in animals with NP. Methods Sixteen male Sprague-Dawley rats were randomly assigned into 4 groups: sham group, spinal nerve ligation (SNL) group as the pain control group, SNL + gingerols-enriched ginger (GEG) extract group, and SNL + shogaols-enriched ginger (SEG) extract group. Animals in GEG and SEG groups were fed their respective diets on the day of SNL surgery for 30 days. At day 30, fecal samples were collected for microbiota composition and functional analyses. 16S rRNA gene sequencing was conducted from fecal samples and microbiome data analysis was performed with QIIME2 and PICRUSt2. Data were analyzed using non-parametric Kruskal–Wallis test to compare GEG and SEG with SNL group. Results Based on the results of alpha-diversity analyses, neither GEG nor SEG treatment affected the evenness of microbiome. Gingerols or shogaols supplementation into the diet reduced the richness of the gut microbiome, compared to the SNL group. Relative to the SNL group, GEG group had an increase in the relative abundance of the genus Faecalitalea, while SEG group had an increase in the relative abundance of the genus Aerococcus and species Bacteroides massiliensis. In comparison to SNL group, both GEG and SEG groups showed a decrease in the relative abundance of the family Muribaculaceae and the genus Rikenellaceae RC9 gut group. Functional profiling results revealed that relative to the SNL group, both GEG and SEG supplementation increased the proportion of biosynthetic pathways related to energy metabolism (i.e., pentose phosphate pathway and sugar degradation) and peptidoglycan biosynthesis. Furthermore, GEG and SEG differentially modified amino acid-related metabolic pathways, i.e., tyrosine degradation, tryptophan biosynthesis, arginine, and ornithine biosynthesis. Conclusions GEG and SEG exhibited differential effects on the microbiome composition and function, suggesting a prebiotic potential for dietary ginger root intake in the management of NP. Funding Sources Texas Tech University Health Sciences Center.

scholarly journals Developmental, Dietary, and Geographical Impacts on Gut Microbiota of Red Swamp Crayfish (Procambarus clarkii)

2020 ◽  
Vol 8 (9) ◽  
pp. 1376
Author(s):  
Zhenting Zhang ◽  
Jiali Liu ◽  
Xuexia Jin ◽  
Chao Liu ◽  
Chenwei Fan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Procambarus Clarkii ◽  
Geographical Location ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Red Swamp Crayfish ◽  
Fermented Feed ◽  
Rrna Gene Sequencing

Red swamp crayfish (Procambarus clarkii) breeding is an important economic mainstay in Hubei province, China. However, information on the gut microbiota of the red swamp crayfish is limited. To address this issue, the effect of developmental stage, diet (fermented or non-fermented feed), and geographical location on the gut microbiota composition in the crayfish was studied via high-throughput 16S rRNA gene sequencing. The results revealed that the dominant phyla in the gut of the crayfish were Proteobacteria, Bacteroidetes,Firmicutes, Tenericutes, and RsaHF231. The alpha diversity showed a declining trend during development, and a highly comparable gut microbiota clustering was identified in a development-dependent manner. The results also revealed that development, followed by diet, is a better key driver for crayfish gut microbiota patterns than geographical location. Notably, the relative abundance of Bacteroidetes was significantly higher in the gut of the crayfish fed with fermented feed than those fed with non-fermented feed, suggesting the fermented feed can be important for the functions (e.g., polysaccharide degradation) of the gut microbiota. In summary, our results revealed the factors shaping gut microbiota of the crayfish and the importance of the fermented feed in crayfish breeding.

PHARMACOKINETICS OF FLORFENICOL AND ITS METABOLITE, FLORFENICOL AMINE, IN RED SWAMP CRAYFISH, PROCAMBARUS CLARKII

2011 ◽  
Vol 35 (2) ◽  
pp. 307-312 ◽  
Author(s):  
Gang-Yi YUE ◽  
Zhi-Xin WU ◽  
Qian YANG ◽  
Yi QU ◽  
Li-Jiao PANG ◽  
...  
Keyword(s):  
Procambarus Clarkii ◽  
Red Swamp Crayfish

scholarly journals The lung–gut axis during viral respiratory infections: the impact of gut dysbiosis on secondary disease outcomes

2021 ◽  
Author(s):  
Valentin Sencio ◽  
Marina Gomes Machado ◽  
François Trottein
Keyword(s):  
Gut Microbiota ◽  
Bacterial Infections ◽  
Respiratory Infections ◽  
Critical Role ◽  
Good Health ◽  
Disease Outcomes ◽  
And Function ◽  
Viral Respiratory Infections ◽  
The Impact ◽  
Viral Respiratory

AbstractBacteria that colonize the human gastrointestinal tract are essential for good health. The gut microbiota has a critical role in pulmonary immunity and host’s defense against viral respiratory infections. The gut microbiota’s composition and function can be profoundly affected in many disease settings, including acute infections, and these changes can aggravate the severity of the disease. Here, we discuss mechanisms by which the gut microbiota arms the lung to control viral respiratory infections. We summarize the impact of viral respiratory infections on the gut microbiota and discuss the potential mechanisms leading to alterations of gut microbiota’s composition and functions. We also discuss the effects of gut microbial imbalance on disease outcomes, including gastrointestinal disorders and secondary bacterial infections. Lastly, we discuss the potential role of the lung–gut axis in coronavirus disease 2019.

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.

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