scholarly journals Variant alpha and beta biodiversity of the genus in dadiah through deep sequencing 16S Ribosomonal RNA genes

2021 ◽  
Vol 888 (1) ◽  
pp. 012040
Author(s):  
H Fatdillah ◽  
Desriani ◽  
S Melia ◽  
N Fitria ◽  
H Morita ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Diversity Index ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Buffalo Milk ◽  
Spontaneous Fermentation ◽  
Β Diversity ◽  
West Sumatra ◽  
16 S Rrna ◽  
Rna Genes

Abstract Dadiah is a traditional spontaneous fermentation of buffalo milk from West Sumatra that doesn’t go through pasteurized stages. The aim of the study is to find out the biodiversity of α and β diversity of the microbiota in the level of the genus in dadiah. The V3 -V4 hypervariable region of the 16 S rRNA deep sequencing was used to the detected genus of bacteria. The available data were analyzed by Alpha Diversity (richness and evenness) and Beta Diversity (Taxonomy Chart Heatmaps). These studies revealed that the most divergent sample is appropriate to C3 with Shanon diversity Index 2.014; meanwhile, the most evenness fit in to B4 with the Simpson diversity index of 0.573. Further, the highest value of the heatmap taxonomic chart on the B4 sample has its place in Lactococcus. There were differences in dadiah microbiota composition among the samples based on different areas. Each sample was found Lactococcus and Lactobacillus with the largest populations.

scholarly journals Incidence and predictive biomarkers of Clostridioides difficile infection in hospitalized patients receiving broad-spectrum antibiotics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Cornelis H. van Werkhoven ◽  
◽  
Annie Ducher ◽  
Matilda Berkell ◽  
Mohamed Mysara ◽  
...  
Keyword(s):  
Diversity Index ◽  
Predictive Biomarkers ◽  
Alpha Diversity ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Randomized Controlled ◽  
Clostridioides Difficile ◽  
Clostridioides Difficile Infection ◽  
Observational Cohort ◽  
16 S Rrna

AbstractTrial enrichment using gut microbiota derived biomarkers by high-risk individuals can improve the feasibility of randomized controlled trials for prevention of Clostridioides difficile infection (CDI). Here, we report in a prospective observational cohort study the incidence of CDI and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients ≥ 50 years receiving newly initiated antibiotic treatment with penicillins plus a beta-lactamase inhibitor, 3rd/4th generation cephalosporins, carbapenems, fluoroquinolones or clindamycin from 34 European hospitals. The estimated 90-day cumulative incidences of a first CDI episode is 1.9% (95% CI 1.1-3.0). Carbapenem treatment (Hazard Ratio (95% CI): 5.3 (1.7-16.6)), toxigenic C. difficile rectal carriage (10.3 (3.2-33.1)), high intestinal abundance of Enterococcus spp. relative to Ruminococcus spp. (5.4 (2.1-18.7)), and low Shannon alpha diversity index as determined by 16 S rRNA gene profiling (9.7 (3.2-29.7)), but not normalized urinary 3-indoxyl sulfate levels, predicts an increased CDI risk.

scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

Diversity metrics, species turnovers and nestedness of bird assemblages in a deep karst sinkhole

2017 ◽  
Vol 63 (2) ◽  
pp. 8-16 ◽  
Author(s):  
Corrado Battisti ◽  
Marco Giardini ◽  
Francesca Marini ◽  
Lorena Di Rocco ◽  
Giuseppe Dodaro ◽  
...  
Keyword(s):  
Species Richness ◽  
Random Distribution ◽  
Diversity Index ◽  
Species Turnover ◽  
Floristic Composition ◽  
Bird Assemblages ◽  
Β Diversity ◽  
Stick Model ◽  
Karst Sinkhole

We reported a study on breeding birds occurring inside an 80 m-deep karst sinkhole, with the characterization of the assemblages recorded along its semi-vertical slopes from the upper edge until the bottom. The internal sides of the sinkhole have been vertically subdivided in four belts about 20 m high. The highest belt (at the upper edge of the cenote) showed the highest values in mean number of bird detections, mean and normalized species richness, and Shannon diversity index. The averaged values of number of detections and species richness significantly differ among belts. Species turnover (Cody’s β-diversity) was maximum between the highest belts. Whittaker plots showed a marked difference among assemblages shaping from broken-stick model to geometric series, and explicited a spatial progressive stress with a disruption in evenness towards the deepest belts. Bird assemblages evidenced a nested subset structure with deeper belts containing successive subsets of the species occurring in the upper belts. We hypothesize that, at least during the daytime in breeding season, the observed non-random distribution of species along the vertical stratification is likely due to (i) the progressive simplification both of the floristic composition and vegetation structure, and (ii) the paucity of sunlight as resources from the upper edge to the inner side of the cenote.

scholarly journals Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

2021 ◽  
Author(s):  
E. D. Baranova ◽  
V. G. Druzhinin ◽  
L. V. Matskova ◽  
P. S. Demenkov ◽  
V. P . Volobaev ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Inflammatory Responses ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cell Lung Carcinoma ◽  
Microbiome Composition ◽  
Β Diversity ◽  
Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

The Affects of Genital Myiasis on the Diversity of Vaginal Flora in Female Bactrian Camels

2021 ◽  
Author(s):  
Likang Zhi ◽  
Dongdong Ai ◽  
Ming Yong ◽  
Huar Bao ◽  
Baoxiang Han ◽  
...  
Keyword(s):  
Diversity Index ◽  
Mechanical Damage ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Vaginal Flora ◽  
Bactrian Camel ◽  
Vaginal Tissue ◽  
Health States ◽  
Significant Difference ◽  
Bactrian Camels

Abstract Background: One of the most important diseases that affect the reproductive organs of Bactrian camels is called Genital Myiasis. It can cause serious mechanical damage to the vaginal tissue of female Bactrian camels. The accumulation of bacteria in the vagina of female camels can affect their health and reproductive ability. The effect of this damage is commonly found in the vaginal flora and vaginal mucosal immune system. Therefore, this research is a study of the diversity of the vaginal flora and the differences between healthy Bactrian camels and those suffering from Genital Myiasis.Results: Vaginal microbiota samples were collected from two groups of female Bactrian camels of the same age. Illumina Miseq was used to sequence V3-V4 hypervariable genes of 16S rRNA in the samples, and the results showed that the vaginal microflora of the infected camel had a significantly greater OTU value. According to the Alpha diversity index and the level of vaginal pH, the diversity index of the infected camel flora were higher than that of the normal camel flora, and the pH were lower than that of the normal camel flora (P=0.006). There was no significant difference between the two groups in the abundance of dominant genera of Bactrian camel vaginal (P＞0.05), indicating that the structure of dominant flora of Bactrian camel vagina had a certain stability.Conclusions: Overall this comparison revealed the differences and similarities between vaginal flora Bactrian camels in various health states. In addition, this data provides a reference point for understanding the types of bacteria that cause genital myiasis that damages healthy development of Bactrian camels.

scholarly journals Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR

2020 ◽  
Vol 6 (4) ◽  
pp. 372
Author(s):  
Sara Franco Ortega ◽  
Ilario Ferrocino ◽  
Ian Adams ◽  
Simone Silvestri ◽  
Davide Spadaro ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Its Region ◽  
Rice Paddy ◽  
Bipolaris Oryzae ◽  
Wiener Diversity Index ◽  
Abundant Otus ◽  
Dna Metabarcoding ◽  
Community Complexity

The airborne mycobiota has been understudied in comparison with the mycobiota present in other agricultural environments. Traditional, culture-based methods allow the study of a small fraction of the organisms present in the atmosphere, thus missing important information. In this study, the aerial mycobiota in a rice paddy has been examined during the cropping season (from June to September 2016) using qPCRs for two important rice pathogens (Pyricularia oryzae and Bipolaris oryzae) and by using DNA metabarcoding of the fungal ITS region. The metabarcoding results demonstrated a higher alpha diversity (Shannon–Wiener diversity index H′ and total number of observed species) at the beginning of the trial (June), suggesting a higher level of community complexity, compared with the end of the season. The main taxa identified by HTS analysis showed a shift in their relative abundance that drove the cluster separation as a function of time and temperature. The most abundant OTUs corresponded to genera such as Cladosporium, Alternaria, Myrothecium, or Pyricularia. Changes in the mycobiota composition were clearly dependent on the average air temperature with a potential impact on disease development in rice. In parallel, oligotyping analysis was performed to obtain a sub-OTU identification which revealed the presence of several oligotypes of Pyricularia and Bipolaris with relative abundance changing during monitoring.

scholarly journals 408 Effect of monensin intake during a stocker phase and subsequent finishing phase on rumen bacterial diversity of beef steers

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 163-164
Author(s):  
Caleb P Weiss ◽  
Paul A Beck ◽  
John T Richeson ◽  
Dexter J Tomczak ◽  
Jianmin Chai ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Pennisetum Glaucum ◽  
Rumen Fluid ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Beef Steers ◽  
Diet Change ◽  
Gluten Feed

Abstract Three monensin levels during a stocker phase (0, 800, 1600 g/ton fed in a free choice mineral) and two levels during finishing [0 (U) or 37.5 mg/kg diet DM (M)] were used to determine the effects of monensin supplementation during a stocker and subsequent finishing phase on rumen bacterial communities of beef steers. Thirty calves were fed pearl millet (Pennisetum glaucum) hay with soybean hull and corn gluten feed supplement (0.5% BW daily, AF basis) or grazed fall wheat pasture (Triticum aestivum) during a stocker phase and then transported 1,067 km to Canyon, TX, for finishing. Rumen fluid was collected on d 0, 28, and the end of the stocker phase (d 85). Samples were also obtained at feedlot d 0, 14, 28, 56, and immediately prior to a diet change to include a beta-adrenergic agonist and before shipping for harvest. Rumen microbiota were characterized by next generation sequencing the 16S v4 hypervariable region with the Illumina MiSeq platform. During the stocker phase, Prevotella and Bacteroidetes were the most dominant genus regardless of diet or treatment. Monensin decreased (P ≤ 0.01) alpha diversity (Shannon Index) for cattle consuming hay on d 28 of the stocker phase. In the feedlot, Prevotella, Lachnospiraceae, and Bacteroidetes were the most abundant genus. Steers that were previously on the 0 and 1600 treatments during the stocker phase and were fed monensin at the feedlot had decreased alpha diversity (P = 0.04) on feedlot d 14 compared to those that did not. Monensin at the feedlot tended to increase alpha diversity on d 28 for cattle previously on the 1600 treatment (P = 0.06), and on d 56 for cattle previously on the 0 treatment (P = 0.06). This experiment provides a better understanding of the effect of monensin on rumen bacterial communities throughout production.

scholarly journals Time-series metabarcoding analysis of zooplankton diversity of the NW Atlantic continental shelf

2019 ◽  
Vol 76 (4) ◽  
pp. 1162-1176 ◽  
Author(s):  
Ann Bucklin ◽  
Heidi D Yeh ◽  
Jennifer M Questel ◽  
David E Richardson ◽  
Bo Reese ◽  
...  
Keyword(s):  
Time Series ◽  
Gulf Of Maine ◽  
Diversity Index ◽  
Hypervariable Region ◽  
Detailed Examination ◽  
Science Center ◽  
Ecosystem Monitoring ◽  
Fisheries Science ◽  
Ocean Ecosystem ◽  
Taxonomic Groups

Abstract Biodiversity of zooplankton is central to the functioning of ocean ecosystems, yet morphological taxonomic analysis requires teams of experts and detailed examination of many samples. Metabarcoding (DNA sequencing of short amplified regions of one or a few genes from environmental samples) is a powerful tool for analysis of the composition and diversity of natural communities. The 18S rRNA V9 hypervariable region was sequenced for 26 zooplankton samples collected from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during ecosystem monitoring surveys by the U.S. Northeast Fisheries Science Center during 2002–2012. A total of 7 648 033 sequences and 22 072 operational taxonomic units (OTUs) were identified and classified into 28 taxonomic groups of plankton. Comparative analysis of molecular (V9 sequence numbers) and morphological (abundance counts) focused on seven taxonomic groups and revealed similar patterns of variation among years and regions. Sequence numbers and abundance counts showed positive correlation for all groups, with significant correlations (p < 0.05) for Calanoida, Gastropoda, and Chaetognatha. Shannon diversity index values calculated using sequence numbers and abundance counts showed highly significant correlation (r = 0.625; p < 0.001) across all regions during 2002–2012. This study demonstrates the potential of metabarcoding for time-series analysis of zooplankton biodiversity, ocean ecosystem assessment, and fisheries management.

scholarly journals PSXIII-29 Farm of origin has a major influence on the colonic microbiome but alterations due to selection for feed efficiency are also evident

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney
Keyword(s):  
Feed Efficiency ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Nutrient Digestibility ◽  
Major Influence ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Selection For

Abstract While the intestinal microbiota is functionally important in nutrient digestibility and animal performance, the role of the microbiome in influencing feed efficiency is not well characterised. The objective of this experiment was to determine the relative influence of feed efficiency and farm of origin on the pig colonic microbiome. Animals were sourced from two geographically distinct locations in Ireland (farm A + B) and evaluated to identify pigs divergent in feed efficiency. The 8 most efficient (LRFI) & 8 least efficient (HRFI) pigs from farm A and 12 LRFI & 12 HRFI pigs from farm B were slaughtered. Colonic digesta was collected for sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed on the Illumina MiSeq. Alpha diversity differed between the farms in this study with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P < 0.05). In agreement with this observation, pigs grouped by farm of origin rather than RFI in the beta diversity analysis. However, despite variation between farms, interesting taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of two families BS11 (P < 0.05) and a tendency towards increased Bacteroidaceae (P < 0.10) relative to the HRFI group. At genus level, the LRFI pigs had a tendency towards increased Bacteroides and CF231 (P < 0.10). In conclusion, while farm of origin has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of feed efficiency status was evident.

Analysis of community composition of biofilms in a submerged filter system for the removal of ammonia and phenol from industrial wastewater

2006 ◽  
Vol 34 (1) ◽  
pp. 165-168 ◽  
Author(s):  
C. Cortés-Lorenzo ◽  
M.L. Molina-Muñoz ◽  
B. Gómez-Villalba ◽  
R. Vilchez ◽  
A. Ramos ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Industrial Wastewater ◽  
Treatment Plant ◽  
Hypervariable Region ◽  
Spatial Diversity ◽  
Rrna Gene ◽  
Plant Laboratory ◽  
Degrading Bacteria ◽  
Gradient Gel Electrophoresis ◽  
16 S Rrna

The bacterial diversity of a submerged filter, used for the removal of ammonia and phenol from an industrial wastewater with high salinity, was studied by a cultivation-independent approach based on PCR/TGGE (temperature-gradient gel electrophoresis). The wastewater treatment plant (laboratory scale) combined the nitrification and denitrification processes and consisted of two separated columns (one anoxic and one aerated) connected through a valve. The spatial diversity of bacterial communities in the plant biofilms was analysed by taking samples at four different heights in the system. TGGE profiles of PCR-amplified sequences of the 16 S rRNA gene (V3-hypervariable region) showed significant variations of the bacterial diversity, mainly depending on the concentration of O2 along the system. Several bands separated by TGGE were reamplified and sequenced, in order to explore the composition of the microbial communities in the biofilms. Most of the sequenced bands (10 out of 13) were closely related to the 16 S rRNA gene of marine α-proteobacteria, mainly grouping in the periphery of the genus Roseobacter. Other sequences were related to those of γ-proteobacteria, the nitrite oxidizer Nitrospira marina and anaerobic phenol-degrading bacteria of the Desulfobacteraceae.

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