Assessment of quality characteristics and bacterial community of modified atmosphere packaged chilled pork loins using 16S rRNA amplicon sequencing analysis

AbstractIn this study, we performed 16S rRNA amplicon sequencing analysis of scalp hair shaft from 109 volunteers, who were surveyed using a questionnaire about daily scalp hair care, and employed multiple statistical analyses to elucidate the factors that contribute to the formation of bacterial community structures on scalp hair shaft. Scalp hair microbiota were found to be specific for each individual. Their microbiota were clearly divided into two clusters. Genus level richness of Pseudomonas (Ps) and Cutibacterium (Cu) contributed to the clusters. The clusters around Pseudomonas and Cutibacterium were named Ps-type and Cu-type, respectively. The host gender influenced the bacterial cell numbers of the major genera that included Cutibacterium, Lawsonella, Moraxella, and Staphylococcus on scalp hair shaft. In addition to host intrinsic factors, extrinsic factors such as hair styling and colouring affected the bacterial cell numbers of the major genera. These factors and chemical treatments, such as bleaching and perming, also affected the Ps-type to Cu-type ratios. These results suggest that bacterial community structures on scalp hair shaft are influenced by both intrinsic and extrinsic factors.

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Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing

PeerJ ◽

10.7717/peerj.4725 ◽

2018 ◽

Vol 6 ◽

pp. e4725 ◽

Cited By ~ 6

Author(s):

Francisca Zepeda-Paulo ◽

Sebastían Ortiz-Martínez ◽

Andrea X. Silva ◽

Blas Lavandero

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Amplicon Sequencing ◽

Aphid Species ◽

Community Diversity ◽

Cereal Aphids ◽

Bacterial Community Diversity ◽

16S Rrna Amplicon Sequencing ◽

Secondary Endosymbiont

Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected. We discuss these results in relation to the bacterial endosymbiont diversity found in other regions of the native and introduced range of S. avenae and R. padi. A similar endosymbiont diversity has been reported for both aphid species in their native range. However, variation in the secondary endosymbiont infection could be observed among the introduced and native populations of the aphid S. avenae, indicating that aphid-endosymbiont associations can vary across the geographic range of an aphid species. In addition, we discuss the potential role of aphids as vectors and/or alternative hosts of phytopathogenic bacteria.

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Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽

10.3390/nu13072414 ◽

2021 ◽

Vol 13 (7) ◽

pp. 2414

Author(s):

Laura Sanjulián ◽

Alexandre Lamas ◽

Rocío Barreiro ◽

Alberto Cepeda ◽

Cristina A. Fente ◽

...

Keyword(s):

Breast Milk ◽

16S Rrna ◽

Human Milk ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Maternal Body Mass Index ◽

16S Rrna Amplicon Sequencing ◽

Spanish Women ◽

Calcium Magnesium ◽

Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

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Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Nature Communications ◽

10.1038/s41467-021-22203-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Caitlin M. Singleton ◽

Francesca Petriglieri ◽

Jannie M. Kristensen ◽

Rasmus H. Kirkegaard ◽

Thomas Y. Michaelsen ◽

...

Keyword(s):

16S Rrna ◽

Wastewater Treatment Plants ◽

In Situ Hybridisation ◽

Amplicon Sequencing ◽

Rrna Genes ◽

Fluorescence In Situ Hybridisation ◽

Sequencing Data ◽

High Quality ◽

16S Rrna Amplicon Sequencing ◽

Long Read

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

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Advantage of 16S rRNA amplicon sequencing in Helicobacter pylori diagnosis

Helicobacter ◽

10.1111/hel.12790 ◽

2021 ◽

Author(s):

Boldbaatar Gantuya ◽

Hashem B. El Serag ◽

Batsaikhan Saruuljavkhlan ◽

Dashdorj Azzaya ◽

Takashi Matsumoto ◽

...

Keyword(s):

Helicobacter Pylori ◽

16S Rrna ◽

Amplicon Sequencing ◽

16S Rrna Amplicon Sequencing

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