scholarly journals High-throughput sequencing analysis of bacterial diversity in raw and pasteurized goat milk

2019 ◽  
Author(s):  
Feng Huang ◽  
Siqi Liu ◽  
Xiaokang Zhou ◽  
Pengfei Wang ◽  
Rengchun He ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Goat Milk ◽  
Raw Milk ◽  
Sequencing Analysis ◽  
Quality And Safety ◽  
Microbial Composition ◽  
High Throughput Dna Sequencing

AbstractThe aim of this study was to evaluate the microbial composition of both raw and pasteurized goat milk using high-throughput DNA sequencing. This analysis revealed that the dominant phylum found in the raw milk was Proteobacteria, and the dominant genus was Kluyvera; Proteobacteria and Kluyvera constituted up to 67.66% and 28.85% of the total bacteria population, respectively. The microorganisms in goat milk predominantly consist of Gram-negative bacteria. Notably, Akkermansia and Faecalibacterium were identified in goat milk for the first time. In addition, the results also indicate that some bacteria in pasteurized goat milk may exist in a viable but nonculturable (VBNC) state. This study provides a theoretical basis that may aid the community in better understanding bacterial diversity in goat milk. The results of this study will help us to improve the quality and safety of goat milk.ImportanceThe microbial diversity in goat milk and pasteurized goat milk at different refrigeration stages was described. Several bacterial species that have not previously been reported in goat milk were identified, including many VBNC bacteria. The findings provided the necessary microbial information for quality and safety of goat milk and dairy products.

scholarly journals Snapshot of Cyprus Raw Goat Milk Bacterial Diversity via 16S rDNA High-Throughput Sequencing; Impact of Cold Storage Conditions

Fermentation ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 100
Author(s):  
Eleni Kamilari ◽  
Dimitrios A. Anagnostopoulos ◽  
Photis Papademas ◽  
Marina Efthymiou ◽  
Svitlana Tretiak ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
Cold Storage ◽  
High Throughput Sequencing ◽  
Goat Milk ◽  
Raw Milk ◽  
Storage Conditions ◽  
Gram Negative ◽  
Milk Samples ◽  
The Impact

In general, it is a common practice among dairy producers to store the milk in the refrigerator directly after milking, in order to preserve it and prevent the development of spoilage microbes. However, the impact of keeping the milk in the refrigerator overnight on milk microbial diversity has been poorly investigated. This study aimed to provide a snapshot of the bacterial composition of goat milk after direct storage at −80 °C and after being kept overnight at 4 °C and then in storage at −80 °, using high-throughput sequencing (HTS). Goat milk samples from four different farms were analyzed, to reveal that milk bacterial diversity differed between the two different storage conditions. Goat milk directly stored at −80 °C was characterized by the presence of the Gram-negative contaminants Pseudomonas and Acinetobacter, in addition to the genera Corynebacterium, Chryseobacterium, Bacteroides and Clostridium. Milk samples that were kept overnight at 4 °C were characterized by a reduction in their bacterial biodiversity and the predominance of the Gram-negative, aerobic Phyllobacterium. Overall, HTS methodologies provide an in-depth identification and characterization of the goat raw milk microbiome. Further, they offer a better understanding of the contribution of cold storage conditions to milk microbiota formation. This study may assist dairy producers in improving raw milk and raw milk cheeses quality and guaranteeing consumers’ safety.

scholarly journals Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. e0230924
Author(s):  
Ao-Nan Xia ◽  
Jun Liu ◽  
Da-Cheng Kang ◽  
Hai-Guang Zhang ◽  
Ru-Hua Zhang ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Analysis

scholarly journals High-Throughput, Sequence-Based Analysis of the Microbiota of Greek Kefir Grains from Two Geographic Regions

2020 ◽  
Vol 58 (2) ◽  
pp. 138-146
Author(s):  
Mary S. Kalamaki ◽  
Apostolos S. Angelidis
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Geographic Origin ◽  
Probiotic Properties ◽  
Sequencing Analysis ◽  
Microbial Composition ◽  
Bacterial Phyla ◽  
Geographic Regions ◽  
Kefir Grains

Research background. Kefir is a natural probiotic drink traditionally produced by milk fermentation using kefir grains. Kefir grains are composed of a complex population of bacteria and yeasts embedded in a polysaccharide-protein matrix. The geographic origin of kefir grains may largely influence their microbial composition and the associated kefir drink properties. Although the detailed bacterial composition of kefir grains from several geographic regions has been reported, to date, analogous data about the microbiome of Greek kefir are lacking. Hence, the aim of this study is to investigate the structure and the diversity of the bacterial community of Greek kefir grains.Experimental approach. The bacterial community structure and diversity of two different kefir grains from distant geographic regions in Greece were examined via high-throughput sequencing analysis, a culture-independent metagenomic approach, targeting the 16S rRNA V4 variable region, in order to gain a deeper understanding of their bacterial population diversities.Results and conclusions. Firmicutes (a phylum that includes lactic acid bacteria) was strikingly dominant amongst the identified bacterial phyla, with over 99 % of the sequences from both kefir grains classified to this phylum. At the family level, Lactobacillaceae sequences accounted for more than 98 % of the operational taxonomic units (OTUs), followed by Ruminococcaceae, Lahnospiraceae, Bacteroidaceae and other bacterial families of lesser abundance. Α relatively small number of bacterial genera dominated, with Lactobacillus kefiranofaciens being the most abundant in both kefir grains (95.0 % of OTUs in kefir A and 96.3 % of OTUs in kefir B). However, a quite variable subdominant population was also present in both grains, including bacterial genera that have been previously associated with the gastrointestinal tract of humans and animals, some of which are believed to possess probiotic properties (Faecalibacterium spp., Bacteroides spp., Blautia spp.). Differences among the bacterial profiles of the two grains were very small indicating a high homogeneity despite the distant geographic origin.Novelty and scientific contribution. This is the first study to deeply explore and report on the bacterial diversity and species richness of Greek kefir.

scholarly journals Using High Throughput DNA Sequencing to Evaluate the Accuracy of Serial Dilution Based Tests of Microbial Activities in Oil Pipelines

2018 ◽  
Author(s):  
K. Khanipov ◽  
G. Golovko ◽  
M. Rojas ◽  
M. Pimenova ◽  
L. Albayrak ◽  
...  
Keyword(s):  
High Throughput ◽  
Biofilm Formation ◽  
High Throughput Sequencing ◽  
Serial Dilution ◽  
Metabolic Function ◽  
Microbial Activities ◽  
Microbial Composition ◽  
Oil Pipelines ◽  
High Throughput Dna Sequencing ◽  
Product Degradation

AbstractMicrobial activities have detrimental effects on industrial infrastructure. If not controlled, microbial presence can result in corrosion, biofilm formation, and product degradation. Serial dilution tests are routinely used for evaluating presence and abundance of microorganisms by diluting samples and culturing microbes in specific media designed to support microorganisms with particular properties, such as sulfate reduction.A high-throughput sequencing approach was used to evaluate changes in microbial composition during four standard serial dilution tests. Analysis of 159 isolates revealed significant differences in the microbial compositions of sequential serial dilution titers and identified several cases where: (a) bacteria known to have a detrimental metabolic function (such as acid production) were lost in the serial dilution medium designed to test for this function; (b) bacteria virtually absent in the original sample became dominant in the serial dilution medium. These observations raise concerns regarding the accuracy and overall usefulness of serial dilution tests.

scholarly journals Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

2013 ◽  
Vol 5 (1) ◽  
pp. 21-25 ◽  
Author(s):  
Yue-Jian Hu ◽  
Qian Wang ◽  
Yun-Tao Jiang ◽  
Rui Ma ◽  
Wen-Wei Xia ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
High Throughput Sequencing

scholarly journals High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Antibiotics ◽  
2018 ◽  
Vol 7 (2) ◽  
pp. 27 ◽  
Author(s):  
Marta Maciejewska ◽  
Magdalena Całusińska ◽  
Luc Cornet ◽  
Delphine Adam ◽  
Igor Pessi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Spatial Diversity ◽  
Sequencing Analysis
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