Influence of Tissue Type on the Bacterial Diversity and Community in Pork Bacon

In current study, bacterial diversity and community in different tissues of pork bacon were determined using high-throughput sequencing. In total, six phyla and 111 bacterial genera were identified. Among them, three dominant genera (Staphylococcus, Acinetobacter, and Macrococcus) were shared by all bacon samples. The linear discriminant analysis showed that 24 bacterial taxa significantly differentiated between the tissues. Results of non-metric Multidimensional Scaling and redundancy analysis showed that physicochemical characteristics of the tissue prominently structured the bacterial communities. Network analysis also illustrated that tissue type was an important factor impacting the bacterial interactions in different types of tissue. The results of current study can add valuable insights to the traditional homemade pork bacon.

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Evaluation of Bacterial Diversity and Quality Features of Traditional Sichuan Bacon from Different Geographical Region

Applied Sciences ◽

10.3390/app11209738 ◽

2021 ◽

Vol 11 (20) ◽

pp. 9738

Author(s):

Song Wang ◽

Xingjie Wang ◽

Wanshu Pan ◽

Aiping Liu ◽

Shuliang Liu ◽

...

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Physicochemical Characteristics ◽

Geographical Regions ◽

Significant Difference ◽

Geographic Regions ◽

Shared Otus ◽

Nitrite Content

Sichuan bacon is one of the most popular types of Chinese bacon in the domestic market. High-throughput sequencing was used to characterize the bacterial diversity of 39 Sichuan bacon samples collected from 3 geographical regions. The results showed that the bacterial diversity of Sichuan bacon in different regions demonstrated certain specificity as well as similarity, and the shared OTUs were close to 81% of the total number in the basin group, mountain group, and plateau group. At the genus level, Staphylococcus is the most dominant genus among the three groups, covering 26.7%, 20.6%, and 22.7%, respectively. Beta diversity shows significant differences in bacterial compositions in different geographic regions, especially for Pseudomonas, Brochothrix, Lactobacillus, Lactococcus, and Enterococcus. Meanwhile, some physicochemical characteristics were analyzed, and a significant difference (p < 0.05) among the three regions was shown in the Aw, pH, and nitrite content, which were significantly correlated with undesired bacteria. This study provides insights into the understanding of the role of bacterial communities in the microbial safety and quality improvement of Sichuan bacon.

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Tissue Type: A Crucial Factor Influencing the Fungal Diversity and Communities in Sichuan Pork Bacon

Frontiers in Microbiology ◽

10.3389/fmicb.2021.655500 ◽

2021 ◽

Vol 12 ◽

Author(s):

Miao Zhang ◽

Haijun Qiao ◽

Weibing Zhang ◽

Zhongming Zhang ◽

Pengchen Wen ◽

...

Keyword(s):

Fungal Diversity ◽

Redundancy Analysis ◽

Fungal Communities ◽

Tissue Type ◽

Isolation And Identification ◽

Linear Discriminant ◽

Identification Of Fungi ◽

Fungal Interactions ◽

Different Tissues ◽

Different Parts

This study aimed to the variations of fungal diversity and community structure in different parts of traditional homemade Sichuan pork bacon. A total of seven phyla and 91 fungal genera were identified. Among them, Ascomycota and Basidiomycota were the first and second most abundant phyla in the bacon tissues. In addition, five dominant genera (Aspergillus, Candida, Debaryomyces, Malassezia, and Penicillium) were shared by all bacon tissues. The numbers of OTUs unique to individual groups were 14, 67, and 65 for the muscle tissue, the adipose tissue, and pork skin, respectively. Linear discriminant analysis showed that a total of 31 taxa significantly differed among the groups. Results of redundancy analysis indicated that fat content, protein content, aw, and pH of bacon tissue shaped the bacon fungal communities. Results of network analysis also indicated that tissue type was a crucial factor influencing the fungal interactions in different tissues. This study can lay a foundation for further isolation and identification of fungi in the product and provides a basis for further research of food health in homemade traditional pork bacon.

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Wide Geographic Distribution of Bacteriophages That Lyse the Same Indigenous Freshwater Isolate (Sphingomonas sp. Strain B18)

Applied and Environmental Microbiology ◽

10.1128/aem.69.4.2395-2398.2003 ◽

2003 ◽

Vol 69 (4) ◽

pp. 2395-2398 ◽

Cited By ~ 16

Author(s):

Arite Wolf ◽

Jutta Wiese ◽

Günter Jost ◽

Karl-Paul Witzel

Keyword(s):

Bacterial Diversity ◽

Geographic Distribution ◽

Broad Spectrum ◽

Bacterial Strain ◽

Bacterial Communities ◽

Restriction Pattern ◽

Aquatic Environments ◽

Aquatic Habitats ◽

Different Types ◽

Wide Geographic Distribution

ABSTRACT An indigenous freshwater bacterium (Sphingomonas sp. strain B18) from Lake Pluβsee (Schleswig-Holstein, Germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. This bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. Phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction pattern. Some phages were widely distributed, while different types coexisted in the same sample. It was concluded that phages could be a major factor in shaping the structure of bacterial communities and maintaining a high bacterial diversity.

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Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius

Scientific Reports ◽

10.1038/s41598-021-90309-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hanan R. Shehata ◽

Subramanyam Ragupathy ◽

Thomas A. Henry ◽

Steven G. Newmaster

Keyword(s):

Functional Diversity ◽

Ginkgo Biloba ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Panax Quinquefolius ◽

Tissue Type ◽

Rrna Gene ◽

Associated Bacteria ◽

Kegg Pathways

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.

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Effects of different vegetable rotations on the rhizosphere bacterial community and tomato growth in a continuous tomato cropping substrate

PLoS ONE ◽

10.1371/journal.pone.0257432 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257432

Author(s):

Li Jin ◽

Jian Lyu ◽

Ning Jin ◽

Jianming Xie ◽

Yue Wu ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Crop Rotation ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Total N ◽

Rhizosphere Bacterial Community ◽

Healthy Growth ◽

Dominant Bacteria

In this study, High throughput sequencing was used to analyze the effects of different vegetable rotations on the rhizosphere bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the rhizosphere bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

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Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

10.21203/rs.3.rs-906889/v1 ◽

2021 ◽

Author(s):

Lidong Lin ◽

Nengfei Wang ◽

Wenbing Han ◽

Botao Zhang ◽

Jiaye Zang ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Operational Taxonomic Units ◽

The Core ◽

Meltwater Runoff ◽

Glacial Runoff ◽

Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

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Temporal and Spatial Characterization of Sediment Bacterial Communities From Lake Wetlands in a Plain River Network Region

10.21203/rs.3.rs-1042496/v1 ◽

2021 ◽

Author(s):

Wei Huang ◽

Chengqi Tu ◽

Zhenghai Jin ◽

Haoran Yang ◽

Changyu Lu ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Redundancy Analysis ◽

Diversity Index ◽

Critical Role ◽

Rrna Gene ◽

Linear Discriminant ◽

Different Seasons ◽

Lake Wetlands ◽

Sediment Bacterial Communities

Abstract Sediment bacterial communities are a vital component of microbial communities in aquatic and terrestrial ecosystems and they play a critical role in lake wetlands. To investigate the effect of season, depth and regional environmental factors on the composition and diversity of bacterial communities in lake wetland sediments, the millions of Illumina reads (16S rRNA gene amplicons) from sediment bacterial communities in different seasons were examined using a technically consistent approach. Results from diversity index, relative abundance, principal component analysis (PCA), redundancy analysis (RDA) and linear discriminant analysis effect size (LEfSe) analysis indicated that the diversity of the bacterial community in summer was generally higher than in other seasons. Proteobacteria was the most abundant phylum in the sediment samples in different seasons (43.15%–57.41%) and different layers (39.66%–77.97%); the autumn sediments were enriched with Firmicutes (5.67%) and Chloroflexi (12.5%); in all four seasons the sediments were enriched with Betaproteobacteria (14.98%–23.45%), Gammaproteobacteria (11.98%–14.36%) and Deltaproteobacteria (8.68%–14.45%). In the bottom sediments (10–25 cm) Chloroflexi were abundant (average value 10.42%), while Bacteroidetes was the dominant phylum in the surface sediments; and redundancy analysis found that total phosphorus (TP) (P = 0.036) was the main environmental factor influencing the sediment bacterial community in different layers. This study provides a reference for further understanding the effects of seasonal changes on sediment microorganisms in lake wetlands.

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High-throughput Sequencing Analysis and Function Prediction of Lung Microbiota in Healthy Rats

International Journal of Healthcare and Medical Sciences ◽

10.32861/ijhms.53.12.17 ◽

2019 ◽

pp. 12-17

Author(s):

Xiaoyu Li ◽

Zhibang Yang ◽

Jia Liu ◽

Ying Jiang

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Bacterial Colonization ◽

Function Prediction ◽

Anatomical Location ◽

Sequencing Analysis ◽

Linear Discriminant ◽

Microbial Distribution ◽

Significant Difference ◽

Different Tissues

To form the basis of a respiratory disease model in rats by investigating the microbial distribution and composition in the lower respiratory tracts of normal rats. Methods: DNA was extracted from the intestine, trachea, bronchus and lung samples collected from healthy rats under sterile conditions. The 16S rDNA V4-V5 region was sequenced using Illumina high-throughput technology. Results: The sequencing results showed that there was no significant difference in abundance and species diversity of microbiota between the lower respiratory and the intestine. The microbiota structure analysis showed samples from lungs and intestinal shared similarity. However, the dominant species at the levels of phylum, family, and genus diverged. The similarity analysis showed that the lung microbiota were different from the intestines. The linear discriminant analysis showed significantly different species in different tissues; function prediction also showed different microbiota function in different tissues. Conclusions: These results suggest that bacterial colonization depends on the sample’s anatomical location. The human pathogen Acinetobacter lwoffii was also detected in the rat lower respiratory tract samples.

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Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

Polish Journal of Microbiology ◽

10.33073/pjm-2020-031 ◽

2020 ◽

Vol 69 (3) ◽

pp. 283-291

Author(s):

XIAOWEI HUO ◽

YUE WANG ◽

DAWEI ZHANG ◽

TING GAO ◽

MENGMENG LIU

Keyword(s):

Bacterial Communities ◽

Endophytic Bacteria ◽

High Throughput Sequencing ◽

Plant Stress ◽

Chinese Herb ◽

Bacterial Consortium ◽

Glehnia Littoralis ◽

Bacterial Structure ◽

The Difference ◽

Different Tissues

Glehnia littoralis is an endangered medicinal plant growing in the coastal ecological environment and plays an important role in coastal ecosystems. The endophytes in the plant have a significant role in promoting plant growth and enhancing plant stress resistance. However, the endophytic bacterial structure associated with halophyte G. littoralis is still not revealed. In this project, the construction and diversity of endophytic bacterial consortium associated with different tissues of G. littoralis were illustrated with high throughput sequencing of the V3-V4 region of the bacterial 16S rRNA. The results resolved that the diversity and richness of endophytic bacteria were significantly higher in root than in leaf and stem. The operational taxonomic units (OTU) analysis demonstrated that the Actinobacteria and Proteobacteria were dominant in all the samples at the phylum level, and Pseudomonas, Bacillus, Rhizobium were the dominant genera. Our results unraveled that the bacterial communities differed among different tissues of G. littoralis. Endophytic bacterial communities in leaf and stem shared more similarity than that in the root. Furthermore, the difference of bacteria community and structure among different tissues were also detected by principal coordinate analysis. Taken altogether, we can conclude that the bacterial communities of different tissues are unique, which could facilitate understanding the diversity of endophytic bacteria in G. littoralis.

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Differences in the soil bacterial community under organic farming and conventional farming modes revealed by 16S rDNA sequencing

10.21203/rs.3.rs-21660/v1 ◽

2020 ◽

Author(s):

Yazhen Yang ◽

Mingke Fang ◽

Meiyan Wu ◽

Huaisheng Zhang ◽

Huizhen Li ◽

...

Keyword(s):

Soil Sample ◽

Bacterial Diversity ◽

Organic Farming ◽

Bacterial Communities ◽

Strong Positive Correlation ◽

Conventional Farming ◽

Available Nitrogen ◽

Linear Discriminant ◽

Rdna Sequencing ◽

Soil Bacterial

Abstract Background The bacterial communities is complex and different in various agricultural ecosystem. In this study, high-throughput Illumina MiSeq sequencing was conducted to assess the differences in soil bacterial communities between organic farming and conventional farming modes. Results A total of 3, 919 operational taxonomic units were identified and classified as 26 phyla, 42 classes, 78 orders, 120 families, 281 genera. The dominant genera were Lysobacter , Pseudomonas , Massilia , Pseudarthrobacter , Ferruginibacter , Flavobacterium , Flavisolibacter , Brevundimonas , Haliangium and Sphingomonas . Analysis of soil bacterial diversity showed that the soil under the organic farming had a greater bacterial diversity than that under the conventional farming. Linear discriminant analysis effect size analysis showed that the major bacterial groups identified in the soil sample CK1 (2015.4) and CK6 (2017.10) under conventional farming mode were largely different from those in the soil sample O6 (2017.10) under organic farming mode. Redundancy analysis demonstrated that available nitrogen was the most important factor regulating bacterial composition under the organic farming mode, followed by soil rapidly available phosphorous and potassium. Massilia , Pseudomonas , Lysobacter and Pseudarthrobacter abundances showed a strong positive correlation with the content of available nitrogen. Conclusions Organic farming could improve soil organic matter, available nitrogen, rapidly available phosphorus and retard soil acidification. This modification of soil can directly or indirectly relate to the bacterial communities in soil. The shifts of bacterial communities were complicated and dynamic with respect to all sorts of the measures of cultivation and management under organic farming mode.

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