scholarly journals Comparison of Fecal Microbiota between German Holstein Dairy Cows with and without Left-Sided Displacement of the Abomasum

2016 ◽  
Vol 54 (4) ◽  
pp. 1140-1143 ◽  
Author(s):  
Eun-Sik Song ◽  
Sang Il Jung ◽  
Hyung-Jin Park ◽  
Kyoung-Won Seo ◽  
Jeong-Hoon Son ◽  
...  
Keyword(s):  
Dairy Cows ◽  
High Performance ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbial Composition ◽  
16S Rrna Gene Analysis ◽  
Bacterial Composition ◽  
Content Type ◽  
Functional Aspects ◽  
Holstein Dairy Cows

One of the most common diseases in high-performance German Holstein dairy cows is left-sided displacement of the abomasum (LDA). Hypomotility of the abomasum is detrimental during the pathogenesis of LDA. It is known that improper interactions between the gut microbiota and the enteric nervous system contribute to dysfunctions of gastrointestinal motility. Therefore, we hypothesized that the gut microbial composition will be different between German Holstein dairy cows with and without LDA. We used 16S rRNA gene analysis to evaluate whether there are any differences in bacterial composition between German Holstein dairy cows with and without LDA. Even though our data are limited to being used to correlate compositional changes with corresponding functional aspects in the pathogenesis of LDA, results from this study show that the fecal microbial compositions of German Holstein dairy cows with LDA shifted and were less diverse than those in normal cows. In particular,Spirochaeteswere absent in cows with LDA.

scholarly journals Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows

2016 ◽  
Vol 62 (6) ◽  
pp. 538-541 ◽  
Author(s):  
Marija Kaevska ◽  
Petra Videnska ◽  
Karel Sedlar ◽  
Iva Bartejsova ◽  
Alena Kralova ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Mycobacterium Avium ◽  
Mycobacterium Avium Subsp ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Bacterial Populations ◽  
Faecal Samples ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
The 16S Rrna Gene

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne’s disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

scholarly journals Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4827 ◽  
Author(s):  
Katti R. Horng ◽  
Holly H. Ganz ◽  
Jonathan A. Eisen ◽  
Stanley L. Marks
Keyword(s):  
Bacterial Diversity ◽  
Storage Temperature ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Fecal Dna ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Dna Concentration ◽  
Dna Preservation ◽  
Preservation Method

Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.

scholarly journals Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

2018 ◽  
Author(s):  
Katti R Horng ◽  
Holly H Ganz ◽  
Jonathan A Eisen ◽  
Stanley L Marks
Keyword(s):  
Bacterial Diversity ◽  
Storage Temperature ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Fecal Dna ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Dna Concentration ◽  
Dna Preservation ◽  
Preservation Method

Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25°C, 4°C, and -80°C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value= 6.87, DF= 3, P<0.001), storage temperature (F-value=1.77, DF= 3, P=0.037), and duration of sample storage (F-value=3.68, DF= 3, P<0.001). Changes in bacterial composition were observed in samples stored in -80°C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF=8.57, P<0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.

scholarly journals Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

2018 ◽  
Author(s):  
Katti R Horng ◽  
Holly H Ganz ◽  
Jonathan A Eisen ◽  
Stanley L Marks
Keyword(s):  
Bacterial Diversity ◽  
Storage Temperature ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Fecal Dna ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Dna Concentration ◽  
Dna Preservation ◽  
Preservation Method

Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25°C, 4°C, and -80°C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value= 6.87, DF= 3, P<0.001), storage temperature (F-value=1.77, DF= 3, P=0.037), and duration of sample storage (F-value=3.68, DF= 3, P<0.001). Changes in bacterial composition were observed in samples stored in -80°C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF=8.57, P<0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.

scholarly journals Gut Microbiome Analysis Identifies Potential Etiological Factors in Acute Gastroenteritis

2018 ◽  
Vol 86 (7) ◽  
pp. e00060-18 ◽  
Author(s):  
Natalia Castaño-Rodríguez ◽  
Alexander P. Underwood ◽  
Juan Merif ◽  
Stephen M. Riordan ◽  
William D. Rawlinson ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Acute Gastroenteritis ◽  
Sequence Similarity ◽  
Amplicon Sequencing ◽  
Gastrointestinal Diseases ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Content Type ◽  
Depth Analysis

ABSTRACT The morbidity and mortality resulting from acute gastroenteritis and associated chronic sequelae represent a substantial burden on health care systems worldwide. Few studies have investigated changes in the gut microbiome following an episode of acute gastroenteritis. By using nondirected 16S rRNA gene amplicon sequencing, the fecal microbiota of 475 patients with acute gastroenteritis was examined. Patient age was correlated with the overall microbial composition, with a decrease in the abundance of Faecalibacterium being observed in older patients. We observed the emergence of a potential Escherichia-Shigella-dominated enterotype in a subset of patients, and this enterotype was predicted to be more proinflammatory than the other common enterotypes, with the latter being dominated by Bacteroides or Faecalibacterium. The increased abundance of Escherichia-Shigella did not appear to be associated with infection with an agent of a similar sequence similarity. Stool color and consistency were associated with the diversity and composition of the microbiome, with deviations from the norm (not brown and solid) showing increases in the abundances of bacteria such as Escherichia-Shigella and Veillonella. Analysis of enriched outliers within the data identified a range of genera previously associated with gastrointestinal diseases, including Treponema, Proteus, Capnocytophaga, Arcobacter, Campylobacter, Haemophilus, Aeromonas, and Pseudomonas. Our data represent the first in-depth analysis of gut microbiota in acute gastroenteritis. Phenotypic changes in stool color and consistency were associated with specific changes in the microbiota. Enriched bacterial taxa were detected in cases where no causative agent was identified by using routine diagnostic tests, suggesting that in the future, microbiome analyses may be utilized to improve diagnostics.

scholarly journals Abrupt Temporal Fluctuations in the Chicken Fecal Microbiota Are Explained by Its Gastrointestinal Origin

2012 ◽  
Vol 78 (8) ◽  
pp. 2941-2948 ◽  
Author(s):  
M. Sekelja ◽  
I. Rud ◽  
S. H. Knutsen ◽  
V. Denstadli ◽  
B. Westereng ◽  
...  
Keyword(s):  
Barrier Function ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Pathogen Transmission ◽  
Rrna Gene ◽  
Multivariate Statistical ◽  
Content Type ◽  
Factors Affecting ◽  
Temporal Fluctuations ◽  
Gastric Barrier

ABSTRACTOne of the main challenges in understanding the composition of fecal microbiota is that it can consist of microbial mixtures originating from different gastrointestinal (GI) segments. Here, we addressed this challenge for broiler chicken feces using a direct 16S rRNA gene-sequencing approach combined with multivariate statistical analyses. Broiler feces were chosen because of easy sampling and the importance for pathogen transmission to the human food chain. Feces were sampled daily for 16 days from chickens with and without a feed structure-induced stimulation of the gastric barrier function. Overall, we found four dominant microbial phylogroups in the feces. Two of the phylogroups were related to clostridia, one to lactobacilli, and one toEscherichia/Shigella. The relative composition of these phylogroups showed apparent stochastic temporal fluctuations in feces. Analyses of dissected chickens at the end of the experiment, however, showed that the two clostridial phylogroups were correlated to the microbiota in the cecum/colon and the small intestine, while the upper gut (crop and gizzard) microbiota was correlated to the lactobacillus phylogroup. In addition, chickens with a stimulated gizzard also showed less of the proximate GI dominating bacterial group in the feces, supporting the importance of the gastric barrier function. In conclusion, our results suggest that GI origin is a main determinant for the chicken fecal microbiota composition. This knowledge will be important for future understanding of factors affecting shedding of both harmful and beneficial gastrointestinal bacteria through feces.

scholarly journals Spatial and Temporal Variations in Pigment and Species Compositions of Snow Algae on Mt. Tateyama in Toyama Prefecture, Japan

2021 ◽  
Vol 12 ◽  
Author(s):  
Tomomi Nakashima ◽  
Jun Uetake ◽  
Takahiro Segawa ◽  
Lenka Procházková ◽  
Akane Tsushima ◽  
...  
Keyword(s):  
High Performance ◽  
Algal Species ◽  
High Performance Liquid Chromatographic ◽  
Temporal Variations ◽  
Algal Community ◽  
Rrna Gene ◽  
Polar Regions ◽  
Dominant Type ◽  
Content Type ◽  
Snow Algae

Snow algae are photosynthetic microbes that inhabit the melting snow surface in alpine and polar regions. We analyzed the pigment and species composition of colored snow collected on Mt. Tateyama in Japan during the melting seasons of 2015 and 2016. High-performance liquid chromatographic analyses of the pigments extracted from the colored snow showed that their composition varied within the study area and were classified into four types: Type A (astaxanthin-monoester dominant), Type B (medium astaxanthin-monoester content), Type C (abundant primary carotenoids and free-astaxanthin), and Type D (abundant primary carotenoids and astaxanthin diesters). Types A and B were most commonly observed in the study area, whereas Types C and D appeared only at specific sites. Analysis of the 18S ribosomal RNA (18S rRNA) gene revealed six major amplicon sequence variants (ASVs) of snow algae, belonging to the Sanguina, Chloromonas, and Chlainomonas groups. The relative abundance of the algal ASVs showed that Sanguina was dominant (&gt;48%) in both Types A and B, suggesting that the difference in astaxanthin abundance between the two types was caused by the production of pigments in the algal cells. The algal community structures of Types C and D differed from those of Types A and B, indicating that the primary carotenoids and astaxanthin diesters were derived from certain algal species in these types. Therefore, astaxanthin-rich Sanguina algae mostly induced the red snow that appeared widely in this alpine area; however, they were partially dominated by Chloromonas or Chlainomonas algae, causing different pigment compositions.

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

scholarly journals Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Anna M. Seekatz ◽  
Matthew K. Schnizlein ◽  
Mark J. Koenigsknecht ◽  
Jason R. Baker ◽  
William L. Hasler ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Upper Gastrointestinal Tract ◽  
Rrna Gene ◽  
Gi Tract ◽  
Microbial Composition ◽  
Content Type ◽  
Healthy Humans ◽  
Health And Disease ◽  
Upper Gastrointestinal ◽  
Over Time

ABSTRACTAlthough the microbiota in the proximal gastrointestinal (GI) tract have been implicated in health and disease, much about these microbes remains understudied compared to those in the distal GI tract. This study characterized the microbiota across multiple proximal GI sites over time in healthy individuals. As part of a study of the pharmacokinetics of oral mesalamine administration, healthy, fasted volunteers (n = 8; 10 observation periods total) were orally intubated with a four-lumen catheter with multiple aspiration ports. Samples were taken from stomach, duodenal, and multiple jejunal sites, sampling hourly (≤7 h) to measure mesalamine (administered att = 0), pH, and 16S rRNA gene-based composition. We observed a predominance ofFirmicutesacross proximal GI sites, with significant variation compared to stool. The microbiota was more similar within individuals over time than between subjects, with the fecal microbiota being unique from that of the small intestine. The stomach and duodenal microbiota displayed highest intraindividual variability compared to jejunal sites, which were more stable across time. We observed significant correlations in the duodenal microbial composition with changes in pH; linear mixed models identified positive correlations with multipleStreptococcusoperational taxonomic units (OTUs) and negative correlations with multiplePrevotellaandPasteurellaceaeOTUs. Few OTUs correlated with mesalamine concentration. The stomach and duodenal microbiota exhibited greater compositional dynamics than the jejunum. Short-term fluctuations in the duodenal microbiota were correlated with pH. Given the unique characteristics and dynamics of the proximal GI tract microbiota, it is important to consider these local environments in health and disease states.IMPORTANCEThe gut microbiota are linked to a variety of gastrointestinal diseases, including inflammatory bowel disease. Despite this importance, microbiota dynamics in the upper gastrointestinal tract are understudied. Our article seeks to understand what factors impact microbiota dynamics in the healthy human upper gut. We found that the upper gastrointestinal tract contains consistently prevalent bacterial OTUs that dominate the overall community. Microbiota variability is highest in the stomach and duodenum and correlates with pH.

scholarly journals Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Shinya Kageyama ◽  
Mikari Asakawa ◽  
Toru Takeshita ◽  
Yukari Ihara ◽  
Shunsuke Kanno ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Bacterial Diversity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Bacterial Composition ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

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