Characterization of Microbial Communities in a Dairy Farm Matrix in Ningxia, China, by 16S rDNA Analysis

A large amount of dairy manure is produced annually in the Ningxia Hui Autonomous Region of China due to the increase in food-producing animal agriculture in this region. The presence of bovine-originated zoonotic, especially human, pathogenic bacteria in untreated manure poses a significant threat to the environment and to public health. However, little is known about the composition, diversity, and abundance of bacterial communities in untreated dairy manure in the Ningxia region. In this study, the microbial community structure of the dairy farm matrix was characterized through 16S rDNA sequencing. The impact of manure treatment methods on bacterial communities was also analyzed. The results showed that the microbial community in dairy manure contained both beneficial bacteria and pathogens, with Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Actinobacteria as dominant phyla. The results also showed the diversity and variety of abundance of zoonotic pathogens among different matrices. The number of pathogens was found to increase significantly in the accumulated but untreated manure, which appeared to be the main matrix of dairy farms that accumulated pathogens including zoonotic pathogens. Findings from this study suggested that farm management, particularly proper treatment of manure, is essential to achieve a shift in the bacterial community composition and a reduction in the environmental load of pathogens including zoonotic pathogens.

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Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2006001000008 ◽

2006 ◽

Vol 41 (10) ◽

pp. 1507-1516 ◽

Cited By ~ 15

Author(s):

Érico Leandro da Silveira ◽

Rodrigo Matheus Pereira ◽

Denilson César Scaquitto ◽

Eliamar Aparecida Nascimbém Pedrinho ◽

Silvana Pómpeia Val-Moraes ◽

...

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Phylogenetic Analyses ◽

Chemical Properties ◽

Pcr Primers ◽

Native Forest ◽

Sequencing Analysis ◽

Soil Dna ◽

Rdna Sequencing ◽

The Impact

Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.

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Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria

Journal of Clinical Laboratory Analysis ◽

10.1002/jcla.21980 ◽

2016 ◽

Vol 30 (6) ◽

pp. 1056-1060 ◽

Cited By ~ 9

Author(s):

Shih Keng Loong ◽

Chee Sieng Khor ◽

Faizatul Lela Jafar ◽

Sazaly AbuBakar

Keyword(s):

16S Rdna ◽

Pathogenic Bacteria ◽

16S Rdna Sequencing ◽

Rdna Sequencing

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Application of 16S rDNA Sequencing Technology in the Analysis of Pathogenic Bacteria in Sputum of Severe Pneumonia

Advances in Microbiology ◽

10.4236/aim.2021.113011 ◽

2021 ◽

Vol 11 (03) ◽

pp. 157-164

Author(s):

Jun Zheng ◽

Juan Zhu ◽

Bin Chen ◽

Lingxiu Chen ◽

Tian Gao ◽

...

Keyword(s):

16S Rdna ◽

Pathogenic Bacteria ◽

Severe Pneumonia ◽

16S Rdna Sequencing ◽

Sequencing Technology ◽

Rdna Sequencing

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Dietary and Developmental Shifts in Butterfly-Associated Bacterial Communities

10.1101/196816 ◽

2017 ◽

Author(s):

Kruttika Phalnikar ◽

Krushnamegh Kunte ◽

Deepa Agashe

Keyword(s):

Bacterial Communities ◽

Bacterial Community Composition ◽

Amplicon Sequencing ◽

Butterfly Species ◽

Species Identity ◽

Active Selection ◽

Key Factor ◽

Host Diet ◽

Taxonomic Groups ◽

The Impact

ABSTRACTBacterial communities associated with insects can substantially influence host ecology, evolution and behavior. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analyzed bacterial communities of 12 butterfly species across different development stages, using 16S rDNA amplicon sequencing. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, very few species showed significant developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species identity and dietary variation across species. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbor distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities.

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Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing

Polish Journal of Microbiology ◽

10.33073/pjm-2015-004 ◽

2015 ◽

Vol 64 (1) ◽

pp. 29-36 ◽

Cited By ~ 10

Author(s):

YA-BING CHEN ◽

DAO-LIANG LAN ◽

CHENG TANG ◽

XIAO-NONG YANG ◽

JIAN LI

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

16S Rdna ◽

Dna Extraction ◽

Extraction Methods ◽

16S Rdna Sequencing ◽

Bead Beating ◽

Rdna Sequencing ◽

Dna Extraction Methods

To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.

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Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

10.21203/rs.2.16025/v1 ◽

2019 ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Bacterial Communities ◽

Shade Tolerance ◽

Rhizosphere Soil ◽

Photosynthetic Capacity ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Soil Bacterial ◽

The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

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Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00635-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hannah E. Pilch ◽

Andrew J. Steinberger ◽

Donald C. Sockett ◽

Nicole Aulik ◽

Garret Suen ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Pathogenic Bacteria ◽

Bacterial Community Composition ◽

Dairy Farm ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Recycling System ◽

Core Microbiota ◽

Relative Abundances

Abstract Background Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. Results Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. Conclusions These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

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Impact of Inoculum Type on the Microbial Community and Power Performance of Urine-Fed Microbial Fuel Cells

Microorganisms ◽

10.3390/microorganisms8121921 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1921

Author(s):

Maria Jose Salar-Garcia ◽

Oluwatosin Obata ◽

Halil Kurt ◽

Kartik Chandran ◽

John Greenman ◽

...

Keyword(s):

Microbial Community ◽

Power Output ◽

Microbial Fuel Cells ◽

Driving Force ◽

Bacterial Community Composition ◽

Power Performance ◽

Different Types ◽

The Impact ◽

Inoculum Type ◽

Anodic Biofilm

Bacteria are the driving force of the microbial fuel cell (MFC) technology, which benefits from their natural ability to degrade organic matter and generate electricity. The development of an efficient anodic biofilm has a significant impact on the power performance of this technology so it is essential to understand the effects of the inoculum nature on the anodic bacterial diversity and establish its relationship with the power performance of the system. Thus, this work aims at analysing the impact of 3 different types of inoculum: (i) stored urine, (ii) sludge and (iii) effluent from a working MFC, on the microbial community of the anodic biofilm and therefore on the power performance of urine-fed ceramic MFCs. The results showed that MFCs inoculated with sludge outperformed the rest and reached a maximum power output of 40.38 mW·m−2anode (1.21 mW). The power performance of these systems increased over time whereas the power output by MFCs inoculated either with stored urine or effluent decreased after day 30. These results are directly related to the establishment and adaptation of the microbial community on the anode during the assay. Results showed the direct relationship between the bacterial community composition, originating from the different inocula, and power generation within the MFCs.

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Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH

Scientifica ◽

10.1155/2018/9230143 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Biji Shibulal ◽

Saif N. Al-Bahry ◽

Yahya M. Al-Wahaibi ◽

Abdulkadir E. Elshafie ◽

Ali S. Al-Bemani ◽

...

Keyword(s):

16S Rdna ◽

Oil Recovery ◽

Heavy Oil ◽

Bacterial Community Composition ◽

Significance Test ◽

Soil Samples ◽

Oil Well ◽

Rdna Sequencing ◽

Significant Difference ◽

Hydrocarbon Utilizing Bacteria

The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis. The present study aims to understand the bacterial community composition from different heavy oil contaminated soil samples collected from geographically related oil well areas in Oman and to identify spore-forming hydrocarbon utilizing cultivable bacteria. V4 region of 16S rDNA gene was the target for Ion PGM™. A total of 825081 raw sequences were obtained from Ion torrent from all the 10 soil samples. The species richness and evenness were found to be moderate in all the samples with four main phyla, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, the most abundant being Firmicutes.Bacillussp. ubiquitously dominated in all samples followed byPaenibacillus, which was followed byBrevibacillus,Planococcus, andFlavobacterium. Principal Coordinate Analysis (PCoA) and UPGMA dendrogram clustered the 10 soil samples into four main groups. Weighted UniFrac significance test determined that there was significant difference in the communities present in soil samples examined. It can be concluded that the microbial community was different in all the 10 soil samples withBacillusandPaenibacillussp. as predominating genus. The 16S rDNA sequencing of cultivable spore-forming bacteria identified the hydrocarbon utilizing bacteria asBacillusandPaenibacillussp. and the nucleotide sequences were submitted to NCBI GenBank under accession numbers KP119097–KP119115.BacillusandPaenibacillussp., which were relatively abundant in the oil fields, can be recommended to be chosen as candidates for hydrocarbon utilization study.

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Persistence, loss and appearance of bacteria upstream and downstream of a river system

Marine and Freshwater Research ◽

10.1071/mf16010 ◽

2017 ◽

Vol 68 (5) ◽

pp. 851 ◽

Cited By ~ 8

Author(s):

Lisa M. Dann ◽

Renee J. Smith ◽

Thomas C. Jeffries ◽

Jody C. McKerral ◽

Peter G. Fairweather ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Anthropogenic Impacts ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Ecosystem Dynamics ◽

Source Tracking ◽

Freshwater Species ◽

Rdna Sequencing

Bacterial taxa shape microbial community composition and influence aquatic ecosystem dynamics. Studies on bacterial persistence in rivers have primarily focussed on microbial-source tracking as an indicator for faecal-source contamination, whereas archetypal freshwater species have received minimal attention. The present study describes the river microbial communities upstream and 3.3km downstream of a small rural town. By 16S rDNA sequencing, we report three patterns in microbial community composition, namely, persistence, loss and appearance. Persistence was observed as 46% inter-site similarity, perhaps owing to generalists that have information lengths that exceed 3.3km and are capable of adapting to system fluctuations. Loss was observed as 10% site exclusivity upstream, perhaps owing to removal processes such as predation and lysis during transport downstream. Last, appearance was observed as 44% site exclusivity downstream, indicating potential anthropogenic impacts from land run-off on bacterial community composition. High multivariate dispersion among downstream samples, as well as overall sample dissimilarity, present as microscale hotspots of discrete Firmicutes and Cyanobacteria species, indicated higher heterogeneity downstream, and therefore increased patchiness from downstream transport and inputs of bacterial genotypes. These findings suggest relativities among three fates for bacterial species of fluvial systems, persistence, loss and appearance, with each having different effects on system dynamics.

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