scholarly journals Effects of respiratory disease on Kele piglets lung microbiome, assessed through 16S rRNA sequencing

2020 ◽  
Vol 13 (9) ◽  
pp. 1970-1981
Author(s):  
Jing Zhang ◽  
Kaizhi Shi ◽  
Jing Wang ◽  
Xiong Zhang ◽  
Chunping Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Respiratory Tract ◽  
Respiratory System ◽  
Respiratory Diseases ◽  
Lavage Fluid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Composition Analysis ◽  
Α Diversity

Background and Aim: Due to the incomplete development of the immune system in immature piglets, the respiratory tract is susceptible to invasion by numerous pathogens that cause a range of potential respiratory diseases. However, few studies have reported the changes in pig lung microorganisms during respiratory infection. Therefore, we aimed to explore the differences in lung environmental microorganisms between healthy piglets and piglets with respiratory diseases. Materials and Methods: Histopathological changes in lung sections were observed in both diseased and healthy pigs. Changes in the composition and abundance of microbiomes in alveolar lavage fluid from eleven 4-week-old Chinese Kele piglets (three clinically healthy and eight diseased) were studied by IonS5TM XL sequencing of the bacterial 16S rRNA genes. Results: Histopathological sections showed that diseased pigs displayed more lung lesions than healthy pigs. Diseased piglets harbored lower bacterial operational taxonomic units, α-diversity, and bacterial community complexity in comparison to healthy piglets. Taxonomic composition analysis showed that in the diseased piglets, the majority of flora was composed of Ureaplasma, Mycoplasma, and Actinobacillus; while Actinobacillus, Sphingomonas, and Stenotrophomonas were dominant in the control group. The abundance of Ureaplasma was significantly higher in ill piglets (p<0.05), and the phylogenetic tree indicated that Ureaplasma was clustered in Ureaplasma diversum, a conditional pathogen that has the potential to affect the swine respiratory system. Conclusion: The results of this study show that the microbial species and structure of piglets' lungs were changed during respiratory tract infection. The finding of Ureaplasma suggested that besides known pathogens such as Mycoplasma and Actinobacillus, unknown pathogens can exist in the respiratory system of diseased pigs and provide a potential basis for clinical treatment.

scholarly journals Characterization of Bioaerosols from Dairy Barns: Reconstructing the Puzzle of Occupational Respiratory Diseases by Using Molecular Approaches

2012 ◽  
Vol 78 (9) ◽  
pp. 3242-3248 ◽  
Author(s):  
Pascale Blais Lecours ◽  
Marc Veillette ◽  
David Marsolais ◽  
Caroline Duchaine
Keyword(s):  
16S Rrna ◽  
Respiratory Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Exact Nature ◽  
Continuous Exposure ◽  
Content Type ◽  
Humoral Immune ◽  
Molecular Approaches ◽  
First Time

ABSTRACTTo understand the etiology of exposure-related diseases and to establish standards for reducing the risks associated with working in contaminated environments, the exact nature of the bioaerosol components must be defined. Molecular biology tools were used to evaluate airborne bacterial and, for the first time, archaeal content of dairy barns. Three air samplers were tested in each of the 13 barns sampled. Up to 106archaeal and 108bacterial 16S rRNA genes per m3of air were detected. Archaeal methanogens, mainlyMethanobrevibacterspecies, were represented.Saccharopolyspora rectivirgula, the causative agent of farmer's lung, was quantified to up to 10716S rRNA genes per m3of air. In addition, a wide variety of bacterial agents were present in our air samples within the high airborne bioaerosol concentration range. Despite recommendations regarding hay preservation and baling conditions, farmers still develop anS. rectivirgula-specific humoral immune response, suggesting intense and continuous exposure. Our results demonstrate the complexity of bioaerosol components in dairy barns which could play a role in occupational respiratory diseases.

scholarly journals Characteristics of gut microbiota in people with obesity

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255446
Author(s):  
Mengmeng Duan ◽  
Yuezhu Wang ◽  
Qiang Zhang ◽  
Rong Zou ◽  
Min Guo ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Sequencing Data ◽  
Genome Database ◽  
Control Subjects ◽  
And Control

Background Obesity is the cause of cardiovascular diseases and other diseases, leading to increased medical costs, and causing a great burden to individuals, families and society. The prevalence of obesity is increasing and has become a global health problem. There is growing evidence that gut microbiota plays an important role in obesity. In this article, we revealed the differences in the gut microbiota between 21 people with obesity and 21 control subjects, and predicted the functional potential changes by 16S rRNA sequencing of the fecal bacteria of the subjects. Methods The raw sequencing data of 21 healthy Beijing volunteers was downloaded from Microbial Genome Database System. Microbial 16S rRNA genes of 21 adults with obesity were sequenced on an Illumina MiSeq instrument and analyzed by using bioinformatics and statistical methods. Results The diversity of gut microbiota in people with obesity decreased significantly. There were significant differences in gut microbiota between the Obesity and Control group at different levels. At the phylum level, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria are significantly different between the Obesity and Control group. In people with obesity, the ratio of Firmicutes/Bacteroidetes decreased significantly. At the genus level, there were significant differences among the 16 major genera, of which four genera Prevotella, Megamonas, Fusobacterium and Blautia increased significantly in people with obesity, while the remaining 12 genera, Faecalibacterium, Lachnospiracea_incertae_sedis, Gemmiger and Clostridium XlVa, etc. decreased significantly. At the species level, nine species including Bacteroides uniformis and Prevotella copri had significant differences. Compared with the control group, subjects with obesity were abnormalities in 57 pathways, mainly in Carbohydrate metabolism and Lipid metabolism. Conclusions Overall, our study revealed differences in the gut microbiota between people with obesity and control subjects, providing novel target for the treatment of individuals with obesity.

scholarly journals Census of the Bacterial Community of the Gypsy Moth Larval Midgut by Using Culturing and Culture-Independent Methods

2004 ◽  
Vol 70 (1) ◽  
pp. 293-300 ◽  
Author(s):  
Nichole A. Broderick ◽  
Kenneth F. Raffa ◽  
Robert M. Goodman ◽  
Jo Handelsman
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Gypsy Moth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Composition Analysis ◽  
White Oak ◽  
Microbial Composition ◽  
Larval Midgut ◽  
Culture Independent

ABSTRACT Little is known about bacteria associated with Lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. We inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (Lymantria dispar L.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. We also examined the effects of diet on microbial composition. Analysis of individual third-instar larvae revealed a high degree of similarity of microbial composition among insects fed on the same diet. DNA sequence analysis indicated that most of the PCR-amplified 16S rRNA genes belong to the γ-Proteobacteria and low G+C gram-positive divisions and that the cultured members represented more than half of the phylotypes identified. Less frequently detected taxa included members of the α-Proteobacterium, Actinobacterium, and Cytophaga/Flexibacter/Bacteroides divisions. The 16S rRNA gene sequences from 7 of the 15 cultured organisms and 8 of the 9 sequences identified by PCR amplification diverged from previously reported bacterial sequences. The microbial composition of midguts differed substantially among larvae feeding on a sterilized artificial diet, aspen, larch, white oak, or willow. 16S rRNA analysis of cultured isolates indicated that an Enterococcus species and culture-independent analysis indicated that an Entbacter sp. were both present in all larvae, regardless of the feeding substrate; the sequences of these two phylotypes varied less than 1% among individual insects. These results provide the first comprehensive description of the microbial diversity of a lepidopteran midgut and demonstrate that the plant species in the diet influences the composition of the gut bacterial community.

Genomic composition of microbiol gingival sulcus and periodontal pockets in young persons

2020 ◽  
Vol 20 (1) ◽  
pp. 19-25
Author(s):  
S. L. S.L. Blashkova ◽  
T. N. Modina ◽  
A. K. Abdrakhmanov ◽  
D. A. Zinecker ◽  
E. V. Mamaeva ◽  
...  
Keyword(s):  
Risk Factors ◽  
Young People ◽  
16S Rrna ◽  
Periodontal Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Periodontal Pocket ◽  
Control Group ◽  
The Republic

Relevance. Risk factors of local importance plays a crucial role in the development of inflammatory periodontal diseases, but the profile of representation and the role of origin microbial markers continues to be refined, what explains the increasing interest by the metagenomic studies. Purpose. To compare the genomic composition of the microbiota of the periodontal sulcus and periodontal pocket by healthy patients with inflammatory periodontal diseases living on the territory of Kazan, the Republic of Tatarstan. Materials and methods. The study included 25 young people (11 boys, 14 girls) aged 18-19 years, with inflammatory periodontal diseases (chronic generalized catarrhal gingivitis (12 people), chronic generalized periodontitis of mild severity (13 people)). The control group consisted of 11 donors without inflammatory periodontal disease.Results. In the present study structures of microbial communities of periodontal spaces has been analyzed with using the sequencing of fragments of bacterial 16s rRNA genes (regions V3 and V4). Results of the analysis allowed to get a real idea of its composition and to determine both known and previously undefined uncultivated phylotypes. Conclusions. It was shown that in the group of the patients with inflammatory periodontal diseases there were identified 183 phylotypes at the level of genus (Mogibacteriacea, TM7 3, Rs–045, Dethiosulfovibrionaceae) relating to 17 phyls (phylum), that is a synonym of type in taxonomy (taxon between Kingdom and class). By the patients with chronic generalized periodontitis of mild severity, it was not possible to reliably isolate the phylotypes present in increased amounts in relation to chronic catarrhal gingivitis; in relation to control – there was a statistically significant increase in the proportion of families Porphyromonadaceae, Peptostreptococcaceae and the proportion of genera Dialister, Filifactor, Parvimonas, Tannerella, Treponema. 

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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 Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Michaela M. Salcher ◽  
Cristiana Callieri ◽  
Atsushi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Regional Scale ◽  
Scale Up ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Long Read

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.

scholarly journals Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site

2005 ◽  
Vol 71 (10) ◽  
pp. 6308-6318 ◽  
Author(s):  
Helen A. Vrionis ◽  
Robert T. Anderson ◽  
Irene Ortiz-Bernad ◽  
Kathleen R. O'Neill ◽  
Charles T. Resch ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acid Volatile Sulfide ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Geochemical Heterogeneity

ABSTRACT The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.

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