Exploring possible associations of the intestine bacterial microbiome with the pre-weaned weight gaining performance of piglets in intensive pig production

Abstract The pre-weaned weight gain is an important performance trait of pigs in intensive pig production. The bacterial microbiome inside the host is vital to host health and growth performance. The purpose of this study was to explore the possible associations of the intestinal microbiome with the pre-weaned weight gain in intensive pig production. In this study, several anatomical sites (jejunum, ileum, cecum, and colon) were examined for bacterial microbiome structure using 16S rRNA V4-V5 region sequencing with Illumina Miseq. The results showed that the microbial richness (estimated by Chao1 index) in jejunum was positively correlated with the pre-weaned weight gain. This study also revealed that the Firmicutes and Bacteroidetes in colon were the weight gaining-related phyla; while the Selenomonas and Moraxella in ileum and the Lactobacillus in both cecum and colon were the weight gaining-related genera for the pre-weaned piglets in intensive pig prodution. Several intra-microbial interactions within commensal microbiome correlated with the pre-weaned weight gain were excavated, as well. Overall, this study provides an expanded view of the commensal bacterial community inside four anatomical intestinal sites of the commercial piglets and the associations of the intestinal microbiome with the pre-weaned weight gaining performance in intensive pig production.

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A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

Scientific Reports ◽

10.1038/s41598-019-53623-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Siwen Deng ◽

Heidi M.-L. Wipf ◽

Grady Pierroz ◽

Ted K. Raab ◽

Rajnish Khanna ◽

...

Keyword(s):

Bacterial Community ◽

Soil Amendment ◽

Bacterial Community Composition ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Microbiome ◽

Plant Growth Promoting ◽

Miseq Platform ◽

Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

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Diversity of the Bacterial Community of Three Soils Revealed by Illumina-Miseq Sequencing of 16S rRNA Gene in the South of Brazzaville, Congo

American Journal of Microbiological Research ◽

10.12691/ajmr-8-4-4 ◽

2020 ◽

Vol 8 (4) ◽

pp. 141-149

Author(s):

Shaloom Teresa MABIALA ◽

Joseph GOMA-TCHIMBAKALA ◽

Emerance Jessica Claire D’Assise GOMA-TCHIMBAKALA ◽

Augustin Aimé LEBONGUY ◽

Alvychelle Benith BANGA

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Illumina Miseq ◽

Rrna Gene ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

The South

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16S rRNA–Based Analysis Reveals Differences in the Bacterial Community Present in Tissues of Choromytilus chorus (Mytilidae, Bivalvia) Grown in an Estuary and a Bay in Southern Chile

Diversity ◽

10.3390/d13050209 ◽

2021 ◽

Vol 13 (5) ◽

pp. 209

Author(s):

Tamara Valenzuela ◽

Joaquin I. Riling ◽

Giovanni Larama ◽

Jacquelinne J. Acuña ◽

Marco Campos ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Venn Diagram ◽

Linear Discriminant ◽

Operational Taxonomic Units ◽

Marine Bivalves ◽

Diagram Analysis

Microbiota associated with bivalves have drawn considerable attention because studies have suggested their relevance to the fitness and growth of marine bivalves. Although the mussel Choromytilus chorus is a valuable resource for Chilean aquaculture and fisheries, its microbiota is still unknown. In this study, the composition and predicted functions of the bacterial community in tissues of C. chorus specimens grown in an estuary (Nehuentue) and a bay (Hueihue) were investigated. Using 16S rRNA genes as targets, the bacterial abundance in tissues was estimated by quantitative PCR and sequenced via Illumina MiSeq. The abundances of bacteria ranged from 103 to 105 copies of 16S rRNA genes g−1 tissue. In the Nehuentue estuary, the bacterial communities in the tissues were dominated by the Tenericutes phylum, whereas the Tenericutes and Proteobacteria phyla dominated in mussels from Hueihue Bay. Higher numbers of operational taxonomic units (OTUs) were observed in tissues from the Nehuentue Estuary than in those from Hueihue Bay. Differences in bacterial community compositions in tissues between both locations were confirmed by nonmetric multidimensional scaling (nMDS) and Venn diagram analysis. In addition, linear discriminant analysis effect size (LEfSe) revealed that the Mollicutes class and Actynomycetales order were key phylotypes in tissues from the Nehuentue Estuary and Hueihue Bay, respectively. Our analysis also predicted a high abundance of sequences assigned to heterotrophy; however, relatively high functional diversity was also found in tissues from Hueihue Bay. This work represents our first attempt to elucidate the C. chorus microbiota in contrasting Chilean aquatic environments.

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Bacterial Community Diversity of Fermented Pepper in Brazzaville Revealed by Illumina Miseq of 16S rRNA Gene

Food and Nutrition Sciences ◽

10.4236/fns.2021.121004 ◽

2021 ◽

Vol 12 (01) ◽

pp. 37-53

Author(s):

Angélique Espérance Lembella Boumba ◽

Augustin Aimé Lebonguy ◽

Joseph Goma-Tchimbakala ◽

Stech Anomene Eckzehel Nzaou ◽

Chancelvie Pahivelle Limingi Polo ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Illumina Miseq ◽

Community Diversity ◽

Rrna Gene ◽

Bacterial Community Diversity

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Microbial communities associated with the camel tick, Hyalomma dromedarii: 16S rRNA gene-based analysis

Scientific Reports ◽

10.1038/s41598-020-74116-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Nighat Perveen ◽

Sabir Bin Muzaffar ◽

Ranjit Vijayan ◽

Mohammad Ali Al-Deeb

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Bacterial Communities ◽

Health Hazard ◽

Illumina Miseq ◽

Blood Feeding ◽

Microbial Interactions ◽

Rrna Gene ◽

Hyalomma Dromedarii

Abstract Hyalomma dromedarii is an important blood-feeding ectoparasite that affects the health of camels. We assessed the profile of bacterial communities associated with H. dromedarii collected from camels in the eastern part of the UAE in 2010 and 2019. A total of 100 partially engorged female ticks were taken from tick samples collected from camels (n = 100; 50/year) and subjected to DNA extraction and sequencing. The 16S rRNA gene was amplified from genomic DNA and sequenced using Illumina MiSeq platform to elucidate the bacterial communities. Principle Coordinates Analysis (PCoA) was conducted to determine patterns of diversity in bacterial communities. In 2010 and 2019, we obtained 899,574 and 781,452 read counts and these formed 371 and 191 operational taxonomic units (OTUs, clustered at 97% similarity), respectively. In both years, twenty-five bacterial families with high relative abundance were detected and the following were the most common: Moraxellaceae, Enterobacteriaceae, Staphylococcaceae, Bacillaceae, Corynebacteriaceae, Flavobacteriaceae, Francisellaceae, Muribaculaceae, Neisseriaceae, and Pseudomonadaceae. Francisellaceae and Enterobacteriaceae coexist in H. dromedarii and we suggest that they thrive under similar conditions and microbial interactions inside the host. Comparisons of diversity indicated that microbial communities differed in terms of richness and evenness between 2010 and 2019, with higher richness but lower evenness in communities in 2010. Principle coordinates analyses showed clear clusters separating microbial communities in 2010 and 2019. The differences in communities suggested that the repertoire of microbial communities have shifted. In particular, the significant increase in dominance of Francisella and the presence of bacterial families containing pathogenic genera shows that H. dromedarii poses a serious health risk to camels and people who interact with them. Thus, it may be wise to introduce active surveillance of key genera that constitute a health hazard in the livestock industry to protect livestock and people.

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A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

Scientific Reports ◽

10.1038/s41598-020-59771-0 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 5

Author(s):

Anders B. Nygaard ◽

Hege S. Tunsjø ◽

Roger Meisal ◽

Colin Charnock

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Rrna Gene ◽

Preliminary Study ◽

Rrna Gene Sequencing ◽

Building Dust

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Specialized Pro-Resolving Mediator Lipidome and 16S rRNA Bacterial Microbiome Data Associated with Human Chronic Rhinosinusitis

Data in Brief ◽

10.1016/j.dib.2021.107023 ◽

2021 ◽

pp. 107023

Author(s):

Thad W. Vickery ◽

Michael Armstrong ◽

Jennifer M. Kofonow ◽

Charles E. Robertson ◽

Miranda E. Kroehl ◽

...

Keyword(s):

16S Rrna ◽

Chronic Rhinosinusitis ◽

Bacterial Microbiome ◽

Microbiome Data

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Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽

10.3390/biology10070569 ◽

2021 ◽

Vol 10 (7) ◽

pp. 569

Author(s):

Chakriya Sansupa ◽

Sara Fareed Mohamed Wahdan ◽

Terd Disayathanoowat ◽

Witoon Purahong

Keyword(s):

Bacterial Community ◽

Forest Soil ◽

Culture Media ◽

Enrichment Culture ◽

Sequence Similarity ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Soil Samples ◽

Enrichment Cultures ◽

Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

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