scholarly journals Fluctuations in the Microbial Community and the Volatile Organic Acids Created During Aerobic Storage of Ground Beef

2019 ◽  
Vol 3 (2) ◽  
Author(s):  
J. R. Levey ◽  
I. Geornaras ◽  
D. Woerner ◽  
J. Prenni ◽  
J. L. Metcalf ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Microbial Community ◽  
16S Rrna ◽  
Shelf Life ◽  
Ground Beef ◽  
Amplicon Sequencing ◽  
16S Rrna Amplicon Sequencing ◽  
Volatile Organic ◽  
Retail Display ◽  
Volatile Organic Acids

ObjectivesDegradation due to microbial and chemical mechanisms occurs throughout the storage life of ground beef. These pathways are intertwined and the microbial community and the volatile organic acids (VOCs) that evolve in ground beef are dynamic. Evaluation of microbial growth using traditional culture-dependent techniques can be misleading due to the presence of unculturable organisms. Therefore, utilizing culture-independent techniques allows for a more thorough understanding of the microbial community within a meat matrix during storage life. The objective of this study was to employ 16s rRNA amplicon sequencing and VOC identification using GC–MS to explore diversity and changes of the microbial community and VOC production during shelf-life of ground beef.Materials and MethodsFinely ground beef (80/20) was procured from beef processing facilities in the West (one lot) and Midwest (two lots). The lots were separated into three physically separate replicates. Ground beef lots were transported in chub packaging to Colorado State University (Fort Collins, CO), and the chubs were stored in the dark at 2°C for either 16/17 d or 23/24 d. After dark storage, chubs were reground, and 454 g fluff-packs were placed on polystyrene trays before overwrapping with polyvinyl chloride film. The trays were placed in retail display cases maintained at 2–4°C for 5 d. Samples were collected every day of retail display for evaluation of the microbial community and VOC development. Following standardized extraction, 16S rRNA amplicon sequencing was used to explore microbial communities. Sequencing data were analyzed using the programs in the QIIME2 (version 2018.4) pipeline. Similarly, volatile organic compounds were extracted prior to analysis of targeted VOCs using a GC–MS. The project was designed as a split-plot design and was analyzed using R packages (version 3.4.3), lme4, lmerTest, and emmeans. Least squares means were separated using an α of 0.05.ResultsThe top orders of bacteria found in the meat samples were from Enterobacteriales, Lactobacillales, and Pseudomonadales. No differences (P ≥ 0.05) in Faith’s Phylogenetic Diversity Index, or a measure of diversity of the bacterial species within a sample, were observed between Days 0, 2, and 4 of retail case display. A targeted analysis identified eighteen VOCs associated with ground beef spoilage. In previous studies, the presence of hexanal, acetoin and acetic acid are identified as spoilage indicators. Hexanal, Acetoin and acetic acid increased (P ≤ 0.05) over the 5 d of retail display.ConclusionThe use of 16s rRNA amplicon sequencing technology is a relatively recent tool that has rapidly advanced the study of microbial deterioration during beef storage and shelf-life. Moreover, the combination of 16s rRNA amplicon sequencing and identification of VOCs in this study, afforded an exploration of the relationship between chemical and biological changes which occur during ground beef storage. These analytical technologies, when used in unison, can highlight the dynamic relationships and evolution of chemical and biological constituents in ground beef. Further research in ground beef shelf-life should incorporate such measures.

scholarly journals Fluctuations in the Microbial Community and the Volatile Organic Acids Created During Aerobic Storage of Ground Beef

2019 ◽  
Vol 3 (2) ◽  
pp. 81-81
Author(s):  
J. R. Levey ◽  
I. Geornaras ◽  
D. Woerner ◽  
J. Prenni ◽  
J. L. Metcalf ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Acids ◽  
Ground Beef ◽  
Volatile Organic ◽  
Volatile Organic Acids

scholarly journals Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

2020 ◽  
Author(s):  
Kimothy L Smith ◽  
Howard A Shuman ◽  
Douglas Findeisen
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Water Samples ◽  
Ad Hoc ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
The Other ◽  
Water Usage ◽  
16S Rrna Amplicon Sequencing ◽  
Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

scholarly journals Comparative Analysis of Chicken Cecal Microbial Diversity and Taxonomic Composition in Response to Dietary Variation using 16S rRNA Amplicon Sequencing

2021 ◽  
Author(s):  
Zubia Rashid ◽  
Muhammad Zubair Yousaf ◽  
Syed Muddassar Hussain Gilani ◽  
Sitwat Zehra ◽  
Ashaq Ali ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Organic Acids ◽  
Microbial Diversity ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Feed Additives ◽  
Poultry Feed ◽  
16S Rrna Amplicon Sequencing

Abstract Antibiotic resistance poses a serious threat to human and animal health. As a consequence, their use in conventional poultry feed may be replaced by non-antibiotic additives (alternatives to antibiotics, ATAs). Phytogenic feed additives and organic acids have been gaining considerable attention that could abate the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. The aim of this study was to evaluate the effects of phytogenic feed additives and organic acids on cecal microbial diversity using 16S rRNA amplicon sequencing of the V3-V4 region. In this study, 240 chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG) and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with an increased microbial diversity in AB, ORG and COM (p < 0.05). The synergistic effects of PHY and ORG increased the population of beneficial bacteria that belonged to the phyla: Firmicutes, Bacteroides and Proteobacteria in the cecum. The presence of the species Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups. In conclusion, treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens.

scholarly journals Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Evan T Saitta ◽  
Renxing Liang ◽  
Maggie CY Lau ◽  
Caleb M Brown ◽  
Nicholas R Longrich ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Open System ◽  
Organic Material ◽  
Organic Molecules ◽  
Soft Tissues ◽  
Amplicon Sequencing ◽  
Chemical Analyses ◽  
16S Rrna Amplicon Sequencing ◽  
Molecular Flux

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These ‘soft tissues’ have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil ‘soft tissues’ differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

scholarly journals 16S rRNA Amplicon Sequencing of Seawater Microbiota from Quintero Bay, Chile, Affected by Oil Spills, Shows the Presence of an Oil-Degrading Marine Bacterial Guild Structured by the Bacterial Genera Alcanivorax, Cobetia, Halomonas, and Oleiphilus

2018 ◽  
Vol 7 (21) ◽  
Author(s):  
Claudia Ibacache-Quiroga ◽  
Juan Ojeda ◽  
M. Alejandro Dinamarca
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Community Structure ◽  
Oil Spills ◽  
Amplicon Sequencing ◽  
Central Coast ◽  
The Past ◽  
16S Rrna Amplicon Sequencing ◽  
Seawater Samples

The Quintero Bay, located along the central coast of Chile, has suffered different oil spills during the past 5 years, impacting marine ecosystems. This report describes the microbial community structure of seawater samples obtained from the Quintero Bay through 16S rRNA amplicon sequencing.

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

Nutrients ◽  
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.

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

2021 ◽  
Vol 12 (1) ◽  
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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