scholarly journals Comparative Analysis of the Fecal Bacterial Microbiota of Wintering Whooper Swans (Cygnus Cygnus)

2021 ◽  
Vol 8 ◽  
Author(s):  
Wenxia Wang ◽  
Songlin Huang ◽  
Liangliang Yang ◽  
Guogang Zhang
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Hiseq ◽  
Linear Discriminant ◽  
Bacterial Microbiota ◽  
And Control

There are many and diverse intestinal microbiota, and they are closely related to various physiological functions of the body. They directly participate in the host's food digestion, nutrient absorption, energy metabolism, immune response, and many other physiological activities and are also related to the occurrence of many diseases. The intestinal microbiota are extremely important for maintaining normal physical health. In order to explore the composition and differences of the intestinal microbiota of whooper swans in different wintering areas, we collected fecal samples of whooper swans in Sanmenxia, Henan, and Rongcheng, Shandong, and we used the Illumina HiSeq platform to perform high-throughput sequencing of bacterial 16S rRNA genes. Comparison between Sanmenxia and Rongcheng showed no significant differences in ACE, Chao 1, Simpson, and Shannon indices (p > 0.05). Beta diversity results showed significant differences in bacterial communities between two groups [analysis of similarity (ANOSIM): R = 0.80, p = 0.011]. Linear discriminant analysis effect size (LEfSe) analysis showed that at the phylum level, the relative abundance of Actinobacteria was significantly higher in Sanmenxia whooper swans than Rongcheng whooper swans. At the genus level, the amount of Psychrobacter and Carnobacterium in Sanmenxia was significantly higher in Rongcheng, while the relative abundance Catellicoccus and Lactobacillus was significantly higher in Rongcheng than in Sanmenxia. This study analyzed the composition, characteristics, and differences of the intestinal microbiota of the whooper swans in different wintering environments and provided theoretical support for further exploring the relationship between the intestinal microbiota of the whooper swans and the external environment. And it played an important role in the overwintering physiology and ecology, population management, and epidemic prevention and control of whooper swans.

scholarly journals Habitat environmental factors influence intestinal microbial diversity of the short-faced moles (Scaptochirus moschata)

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lei Chen ◽  
Di Xu ◽  
Jing Zhu ◽  
Shen Wang ◽  
Mi Liu ◽  
...  
Keyword(s):  
Information Processing ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Ecological Adaptation ◽  
Functional Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Hiseq ◽  
Intestinal Microbes ◽  
Sequencing Platform

AbstractThe short-faced moles (Scaptochirus moschata) are unique Chinese mammal that live in burrows for life. They have complex ecological adaptation mechanisms to adapt to perennial underground life. Intestinal microbes play an important role in the ecological adaptation of wild animals. The gut microbiota diversity and its function in short-faced moles’ ecological adaptation is a scientific issue worth exploring. In this study, the Illumina HiSeq sequencing platform was used to sequence the V3-V4 hypervariable regions of the 16S rRNA genes of 22 short-faced moles’ intestinal samples to study the composition and functional structure of their intestinal microbiota. The results showed that in the short-faced moles’ intestine, there are four main phyla, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidete. At the family level, Peptostreptococcaceae and Enterobacteriaceae have the highest abundance. At the genus level, Romboutsia is the genus with the highest microbial abundance. According to the KEGG database, the main functions of short-faced mole gut microbes are metabolism, genetic information processing, environmental information processing, and cellular processes. The function of short-faced mole intestinal microbiota is suitable for its long-term burrowing life. No gender difference is found in the composition and function of the short-faced mole intestinal microbiota. There are significant differences in the composition and functional structure of the short-faced mole gut microbiota between samples collected from different habitats. We conferred that this is related to the different environment factors in which they live, especially to the edaphic factors.

scholarly journals Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1401
Author(s):  
Sergei Sokolov ◽  
Ksenia Fursova ◽  
Irina Shulcheva ◽  
Daria Nikanova ◽  
Olga Artyemieva ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bovine Mastitis ◽  
Principal Component ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Linear Discriminant ◽  
Milk Samples ◽  
Central Russia ◽  
Animal Populations ◽  
Significant Difference

Bovine mastitis is a widespread infectious disease. In addition to the economic damages associated with reduced milk yield due to mastitis, the problem of food contamination by microorganism metabolites, in particular toxins, is also a concern. Horizontal transfer of microorganisms from animal populations to humans can also be complicated by antibiotic resistance. Therefore, bovine mastitis is relevant to the study of microbiology and veterinary medicine. In this study, we investigated the microbiome of milk samples from healthy cows and cows with different forms of mastitis from individual quarters of the udder of cows during first and second lactation. Total DNA was extracted from milk samples. The V3–V4 regions of the bacterial 16S rRNA genes from each sample were amplified to generate a library via high-throughput sequencing. We revealed significant dominance of several operational taxonomic units (OTUs) corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. In addition, we unexpectedly identified Streptococcus thermophilus in samples with high SCC quantities. We found some infectious agents that characterized summer mastitis. We demonstrated that in Central Russia, mastitis is associated with a wide variety of causal organisms. We observed some differences in the diversity of the two investigated farms. However, we did not find any significant difference among healthy, mastitis and subclinical samples according to their SCC status from either farms by principal component analysis. Linear discriminant analysis effect size (LEfSe) confirmed the presence of several indicator genera in farms from Moscow and the Tula Region. These results confirm the complex bacterial etiology of bovine mastitis.

scholarly journals Changes in the Phenolic Fraction of Protobind 1000 and Bacterial Microbiota in the Gut of a Higher Termite, Nasutitermes Ephratae

2020 ◽  
Vol 5 (3) ◽  
pp. 1-11
Author(s):  
Miambi E
Keyword(s):  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gas Chromatography Mass Spectrometry ◽  
Termite Species ◽  
Pyrolysis Gas ◽  
Phenolic Fraction ◽  
Bacterial Microbiota ◽  
Soda Lignin ◽  
Worker Caste

Termites are examples of natural biomass utilization systems that have evolved to overcome the recalcitrance of lignin to degradation. To investigate the application of this to the conversion of technical lignins produced by biorefineries, a higher wood-feeding termite species, Nasutitermes ephratae, was fed with a commercial grass soda lignin (Protobind 1000, PB1000). We investigated the fate of PB1000 in termite guts and the changes in gut microbiota that occurred using Pyrolysis - Gas Chromatography / Mass Spectrometry (Py-GC/MS) and high-throughput sequencing of the 16S rRNA genes. The worker caste termites fed with PB1000 had only half the survival rate of the controls and increased the PB1000 syringyl/guaiacyl ratio from 1.74 to 2.26. The changes in the syringyl/guaiacyl ratio were consistent with the degradation of the free phenolic monomers in PB1000 inside the termite gut, and they were associated with the increase in the relative abundance of Firmicutes and Bacteroidetes. This work showed the ability of the digestive tract of a wood-feeding higher termite species, N. ephratae, to metabolize the free-volatile phenolic monomers in PB1000. Overall, our results identified bacterial candidates for the development of a bacterial inoculum in pretreatment processes for the utilization of technical lignin in biorefineries.

scholarly journals Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski’s horses in China

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251512
Author(s):  
Dini Hu ◽  
Yuzhu Chao ◽  
Boru Zhang ◽  
Chen Wang ◽  
Yingjie Qi ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Sequence Data ◽  
Parasitic Infection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bioinformatics Analyses ◽  
Gasterophilus Pecorum ◽  
First Time

Horse botflies have been a threat to the Przewalski’s horses in the Kalamaili Nature Reserve in Xinjiang of China since their reintroduction to the original range. As larvae of these parasites could infest the intestine of a horse for months, they could interact with and alter the structure and composition of its intestinal microbiota, affecting adversely its health. Nonetheless, there are no such studies on the rewilded Przewalski’s horses yet. For the first time, this study characterizes the composition of the intestinal microbiota of 7 rewilded Przewalski’s horses infected severely by Gasterophilus pecorum following and prior to their anthelmintic treatment. Bioinformatics analyses of the sequence data obtained by amplicon high throughput sequencing of bacterial 16S rRNA genes showed that G. pecorum infestation significantly increased the richness of the intestinal microbial community but not its diversity. Firmicutes and Bacteroidetes were found the dominant phyla as in other animals, and the parasitic infestation decreased the F/B ratio largely by over 50%. Large reduction in relative abundances of the two genera Streptococcus and Lactobacillus observed with G. pecorum infestation suggested possible changes in colic and digestion related conditions of the infected horses. Variations on the relative abundance of the genus groups known to be pathogenic or symbiotic showed that adverse impact of the G. pecorum infestation could be associated with reduction of the symbiotic genera Lactobacillus and Bifidobacterium that are probiotics and able to promote immunity against parasitic infection.

scholarly journals Habitat environmental factors and gender influence intestinal microbial diversity of the short-faced moles (Scaptochirus moschata)

2021 ◽  
Author(s):  
Lei Chen ◽  
Di Xu ◽  
Jing Zhu ◽  
Shen Wang ◽  
Mi Liu ◽  
...  
Keyword(s):  
Information Processing ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Ecological Adaptation ◽  
Functional Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Hiseq ◽  
Intestinal Microbes ◽  
Sequencing Platform

Abstract The short-faced moles (Scaptochirus moschata) are unique Chinese mammal that live in burrows for life. They have complex ecological adaptation mechanisms to adapt to perennial underground life. Intestinal microbes play an important role in the ecological adaptation of wild animals. The gut microbiota diversity and its function in short-faced moles’ ecological adaptation is a scientific issue worth exploring. In this study, the Illumina HiSeq sequencing platform was used to sequence the V3-V4 hypervariable regions of the 16S rRNA genes of 22 short-faced moles’ intestinal samples to study the composition and functional structure of their intestinal microbiota. The results showed that in the short-faced moles’ intestine, there are four main phyla, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidete. At the family level, Peptostreptococcaceae and Enterobacteriaceae have the highest abundance. At the genus level, Romboutsia is the genus with the highest microbial abundance. According to the KEGG database, the main functions of short-faced mole gut microbes are metabolism, genetic information processing, environmental information processing, and cellular processes. The function of short-faced mole intestinal microbiota is suitable for its long-term burrowing life. No gender difference is found in the composition and function of the short-faced mole intestinal microbiota. There are significant differences in the composition and functional structure of the short-faced mole gut microbiota between samples collected from different habitats. We conferred that this is related to the different environment factors in which they live, especially to the edaphic factors.

Endophytic Microbiota Comparison of Dendrobium huoshanense Root and Stem in Different Growth Years

Planta Medica ◽  
2019 ◽  
Vol 86 (13/14) ◽  
pp. 967-975
Author(s):  
Shaotong Chen ◽  
Jun Dai ◽  
Xiangwen Song ◽  
Xueping Jiang ◽  
Qun Zhao ◽  
...  
Keyword(s):  
Medicinal Plants ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Size Analysis ◽  
Linear Discriminant ◽  
Bacterial Phyla ◽  
Microbe Interactions ◽  
Dendrobium Huoshanense

AbstractThe endophytic microbiome in medicinal plants is rich and diverse, but few studies have followed the endophytic microbiome of medicinal plants in different tissues with their growth. In this study, we examined the endophytic bacterial and fungal community structures associated with both the stem and root compartments of Dendrobium huoshanense at different growth years via high-throughput sequencing of 16S rRNA genes and nrDNA fragments of internal transcribed spacer regions. Results indicated that more diverse prokaryotic and fungal operational taxonomic units were detected in roots than in stems, and the alpha diversity of endophytic prokaryotic significantly differed among the 1-, 2-, and 3-year-old roots. The dominant bacterial phyla Proteobacteria Firmicutes, Actinobacteria, Bacteroidetes, and Acidobacteria, and fungal phyla Ascomycota, Basidiomycota, and Ascomycota were detected in the stems and roots with 3 growth years. Moreover, linear discriminant effect size analysis revealed 138 differentially abundant taxonomic clades in the bacterial level, and 197 in the fungal level in six groups. Our results provide evidence for endophytic microbiota communities depending on the tissues and growth years of D. huoshanense. The results from this study should be useful to better understand medicinal plant-microbe interactions.

scholarly journals Intestinal microbiota changes in Graves’ disease: a prospective clinical study

2020 ◽  
Vol 40 (9) ◽  
Author(s):  
Hui-xian Yan ◽  
Wen-cheng An ◽  
Fang Chen ◽  
Bo An ◽  
Yue Pan ◽  
...  
Keyword(s):  
16S Rrna ◽  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Prospective Clinical Study ◽  
Graves Disease ◽  
Healthy Controls ◽  
Sample Collection

Abstract Graves’ disease (GD) occurs due to an autoimmune dysfunction of thyroid gland cells, leading to manifestations consistent with hyperthyroidism. Various studies have confirmed the link between autoimmune conditions and changes in the composition of intestinal microbial organisms. However, few studies have assessed the relationship between the GD and the changes in intestinal microbiota. Therefore, the present study aimed to investigate changes in intestinal flora that may occur in the setting of GD. Thirty-nine patients with GD and 17 healthy controls were enrolled for fecal sample collection. 16S rRNA sequencing was used to analyze the diversity and composition of the intestinal microbiota. High-throughput sequencing of 16S rRNA genes of intestinal flora was performed on Illumina Hiseq2500 platform. Comparing to healthy individuals, the number of Bacilli, Lactobacillales, Prevotella, Megamonas and Veillonella strains were increased, whereas the number of Ruminococcus, Rikenellaceae and Alistipes strains were decreased among patients with GD. Furthermore, patients with GD showed a decrease in intestinal microbial diversity. Therefore, it indicates that the diversity of microbial strains is significantly reduced in GD patients, and patients with GD will undergo significant changes in intestinal microbiota, by comparing the intestinal flora of GD and healthy controls. These conclusions are expected to provide a preliminary reference for further researches on the interaction mechanism between intestinal flora and GD.

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

2021 ◽  
Vol 9 (3) ◽  
pp. 617
Author(s):  
Zhenbing Wu ◽  
Qianqian Zhang ◽  
Yaoyao Lin ◽  
Jingwen Hao ◽  
Shuyi Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
High Throughput Sequencing ◽  
Gas Chromatography Mass Spectrometry ◽  
Gastrointestinal Mucosa ◽  
Gastrointestinal Microbiota ◽  
Linear Discriminant ◽  
Intestinal Microbes ◽  
Nile Tilapia Oreochromis Niloticus

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia–Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia–Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

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