scholarly journals Unveiling the Bovine Epimural Microbiota Composition and Putative Function

2021 ◽  
Vol 9 (2) ◽  
pp. 342
Author(s):  
Cátia Pacífico ◽  
Renée Maxine Petri ◽  
Sara Ricci ◽  
Elsayed Mickdam ◽  
Stefanie Urimare Wetzels ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Gene Target ◽  
Functional Potential ◽  
Metabolic Functions ◽  
Sources Of Variation ◽  
Experimental Protocols ◽  
Biological Sources ◽  
The 16S Rrna Gene

Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.

scholarly journals Gut Microbiota Analysis Results Are Highly Dependent on the 16S rRNA Gene Target Region, Whereas the Impact of DNA Extraction Is Minor

2017 ◽  
Vol 28 (1) ◽  
pp. 19-30 ◽  
Author(s):  
Anniina Rintala ◽  
Sami Pietilä ◽  
Eveliina Munukka ◽  
Erkki Eerola ◽  
Juha-Pekka Pursiheimo ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Rrna Gene ◽  
Gene Target ◽  
Target Region ◽  
Microbiota Analysis ◽  
The Impact ◽  
The 16S Rrna Gene

scholarly journals Developmental differences in the intestinal microbiota of Chinese 1-year-old infants and 4-year-old children

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Min Guo ◽  
Maohua Miao ◽  
Yuezhu Wang ◽  
Mengmeng Duan ◽  
Fen Yang ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Gut Microbiota ◽  
Hypervariable Region ◽  
Functional Change ◽  
Developmental Differences ◽  
Species Level ◽  
Infant Food ◽  
Rrna Gene ◽  
High Throughput Dna Sequencing ◽  
The 16S Rrna Gene

Abstract The microbiota profile of children changes with age. To investigate the differences in the gut microbiota profile of 1- and 4-year-old children, we collected fecal samples and sequenced the V3–V4 hypervariable region of the 16S rRNA gene via high-throughput DNA sequencing. From phylum to species level, the microbiota underwent significant changes with age. The abundance of phyla Proteobacteria and Actinobacteria declined with age, whereas phyla Firmicutes and Bacteroidetes increased with age and dominated the gut microbiota of 4-year-olds. The intestinal environment of children at age four is closer to maturity. Hence, the abundance of Bifidobacterium significantly decreased in the gut of 4-year-olds, whereas Akkermansia muciniphila increased from 0.14% in 1-year-olds to 4.25% in 4-year-olds. The functional change in gut microbiota is consistent with changes in infant food, as microbiota participating in amino acid and vitamin metabolism were enriched in 1-year-olds, whereas microbiota involved in lipid metabolism increased with age.

scholarly journals Bacteria associated with the intestinal tract of three predators of Dactylopius opuntiae (Hemiptera: Dactylopiidae)

2021 ◽  
Author(s):  
Susana Martínez-Martínez ◽  
Esteban Rodríguez-Leyva ◽  
Sergio Aranda-Ocampo ◽  
Ma.Teresa Santillán-Galicia ◽  
Antonio Hernández-López ◽  
...  
Keyword(s):  
Intestinal Tract ◽  
Bacillus Pumilus ◽  
Carminic Acid ◽  
Rrna Gene ◽  
Average Content ◽  
Partial Sequencing ◽  
Metabolic Functions ◽  
Enterococcus Gallinarum ◽  
The 16S Rrna Gene

Abstract Insects depend on gut bacteria for many metabolic functions including detoxification. Dactylopius (Hemiptera: Dactylopiidae) species (e.g. D. opuntiae and D. coccus) produce carminic acid possibly acting as part of their immune response to predation; thus predators of Dactylopius species may require intestinal symbionts to metabolize carminic acid acquired from their prey. The average content of carminic acid in D. opuntiae and D. coccus is 3–5% and 19–25% respectively; the predators Leucopina bellula and Hyperaspis trifurcata are specialists on D. opuntiae while Laetilia coccidivora feeds on both D. opuntiae and D. coccus. We determined the diversity of bacteria associated with the gut of these predators to test the hypothesis that it would vary significantly depending on the level of prey specialism. Bacteria were isolated from the intestine of Le. bellula, L. coccidivora and H. trifurcata larvae and also adults of H. trifurcata. Bacteria were identified morphologically and by partial sequencing of the 16S rRNA gene. The greatest bacterial diversity was found in L. coccidivora and H. trifurcata adults, followed by H. trifurcata larvae. The lowest diversity was found in Le. bellula. Sequencing revealed the presence of Bacillus cereus, Enterococcus gallinarum and E. casseliflavus in L. coccidivora larvae; Enterobacter sp. in larvae of H. trifurcata; Lactococcus lactis in adults of H. trifurcate; and Staphylococcus sp. in larvae and adults of H. trifurcate. Bacillus pumilus was only found in Le. bellula. The possible role of these bacteria in the ability of predators to feed on D. opuntiae and D. coccus is discussed.

scholarly journals Changes in the diversity and composition of gut microbiota in pigeon squabs infected with Trichomonas gallinae

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Feng Ji ◽  
Dongyan Zhang ◽  
Yuxin Shao ◽  
Xiaohan Yu ◽  
Xiaoyong Liu ◽  
...  
Keyword(s):  
Small Intestine ◽  
Gut Microbiota ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Low Grade ◽  
Gi Tract ◽  
Trichomonas Gallinae ◽  
Altricial Birds ◽  
Microbiota Diversity ◽  
The 16S Rrna Gene

AbstractPigeons, as the only altricial birds in poultry, are the primary Trichomonas gallinae (T. gallinae) host. To study the effects of T. gallinae infection on gut microbiota, we compared the microbiota diversity and composition in gastrointestinal (GI) tracts of pigeons at the age of 14 and 21 day with different degrees of T. gallinae infection. Thirty-six nestling pigeons were divided into three groups: the healthy group, low-grade and high-grade trichomonosis group. Then, the crop, small intestine and rectum contents were obtained for sequencing of the 16S rRNA gene V3–V4 hypervariable region. The results showed that the microbiota diversity was higher in crop than in small intestine and rectum, and the abundance of Lactobacillus genus was dominant in small intestine and rectum of healthy pigeons at 21 days. T. gallinae infection decreased the microbiota richness in crop at 14 days. The abundance of the Firmicutes phylum and Lactobacillus genus in small intestine of birds at 21 days were decreased by infection, however the abundances of Proteobacteria phylum and Enterococcus, Atopobium, Roseburia, Aeriscardovia and Peptostreptococcus genus increased. The above results indicated that crop had the highest microbiota diversity among GI tract of pigeons, and the gut microbiota diversity and composition of pigeon squabs were altered by T. gallinae infection.

scholarly journals Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11827
Author(s):  
Estefanía Garibay-Valdez ◽  
Francesco Cicala ◽  
Marcel Martinez-Porchas ◽  
Ricardo Gómez-Reyes ◽  
Francisco Vargas-Albores ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Structural Changes ◽  
Hypervariable Region ◽  
White Shrimp ◽  
Rrna Gene ◽  
Functional Capabilities ◽  
Metabolic Functions ◽  
Longitudinal Variations ◽  
Dominant Bacteria ◽  
Differential Abundance Analysis

The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Mohamed Zeineldin ◽  
Ahmed A. Elolimy ◽  
Radwa Barakat
Keyword(s):  
16S Rrna ◽  
Respiratory Tract ◽  
Respiratory Health ◽  
Meta Analysis ◽  
Hypervariable Region ◽  
Diversity Indices ◽  
Feedlot Cattle ◽  
Rrna Gene ◽  
Significant Difference ◽  
Respiratory Microbiota

ABSTRACT Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between healthy calves and those that developed bovine respiratory disease (BRD). Our results showed that the overall composition and diversity of respiratory microbiota in cattle were significantly affected by study design, 16S rRNA hypervariable region sequenced, health status, time since arrival to the feedlot, sampling sites in the respiratory tract and antibiotic treatment. Assessment of diversity indices showed a statistically significant difference between the BRD-affected cattle and healthy control calves. Using multivariate network analysis and Spearman's correlation analyses, we further distinguished the taxa that were commonly associated with BRD when the day of arrival to the feedlot was added to the model. The probability of being identified as BRD was significantly correlated with days 7, 12 and 14 following the calf's arrival to the feedlot. These findings could help in proposing strategies to further evaluate the link between respiratory microbiota and bovine respiratory health.

scholarly journals Characterization of bacterial communities associated with blood-fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Li Lim ◽  
Abdul Hafiz Ab Majid
Keyword(s):  
Microbial Community ◽  
Bacterial Communities ◽  
Hypervariable Region ◽  
Cimex Lectularius ◽  
Rrna Gene ◽  
Bed Bugs ◽  
Cimex Hemipterus ◽  
The 16S Rrna Gene ◽  
Bacteria Communities

AbstractWith the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well-studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood-fed and starved tropical bed bugs were analysed and characterized by amplifying the v3-v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha-proteobacterium Wolbachia and gamma-proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood-fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood-fed bed bugs.

Novel Streptomyces sp. reported in 2018: A meta-analysis

2020 ◽  
Vol 18 ◽  
Author(s):  
Sagar Aryal ◽  
Laxmi Neupane ◽  
Rameshwar Adhikari ◽  
Balmukunda Regmi ◽  
Niranjan Koirala ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Meta Analysis ◽  
Antimicrobial Properties ◽  
Data Entry ◽  
Flow Diagram ◽  
Rrna Gene ◽  
Research Papers ◽  
Biosynthesis Gene Cluster ◽  
Streptomyces Species ◽  
Sugar Fermentation

: Streptomyces species are very well known for the production of antimicrobials and enzymes. The objective of this review is to search for the novel Streptomyces isolated in 2018 along with their characteristics and possible antimicrobial properties. The literature search was done according to the PRISMA flow diagram where 28 research papers were eligible for the review. Data entry and analyses were performed using IBM SPSS Statistics version 25 while phylogenetic tree was constructed using Geneious Prime Software. The data on general characteristics, biochemical as well as sugar fermentation tests, 16S rRNA gene sequence similarity and DNA-DNA hybridization relatedness were extracted from the research papers and summarized in tables and figures. The biosynthesis gene cluster (BGC) was identified using ‘antibiotics and secondary metabolite analysis shell-antiSMASH’ which showed the possibility of production of new antibiotics, antifungal and antitumor substances from the 28 novel Streptomyces isolated in 2018 which would contribute to the global effort to fight against growing multidrug-resistance.

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

scholarly journals A Novel Microbial Zearalenone Transformation through Phosphorylation

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 294
Author(s):  
Yan Zhu ◽  
Pascal Drouin ◽  
Dion Lepp ◽  
Xiu-Zhen Li ◽  
Honghui Zhu ◽  
...  
Keyword(s):  
Microbial Transformation ◽  
Acid Tolerance ◽  
Transformation Product ◽  
The United States ◽  
Corn Silage ◽  
Rrna Gene ◽  
Bacillus Spp ◽  
High Concentrations ◽  
The 16S Rrna Gene ◽  
Bacillus Strains

Zearalenone (ZEA) is a mycotoxin widely occurring in many agricultural commodities. In this study, a purified bacterial isolate, Bacillus sp. S62-W, obtained from one of 104 corn silage samples from various silos located in the United States, exhibited activity to transform the mycotoxin ZEA. A novel microbial transformation product, ZEA-14-phosphate, was detected, purified, and identified by HPLC, LC-MS, and NMR analyses. The isolate has been identified as belonging to the genus Bacillus according to phylogenetic analysis of the 16S rRNA gene and whole genome alignments. The isolate showed high efficacy in transforming ZEA to ZEA-14-phosphate (100% transformation within 24 h) and possessed advantages of acid tolerance (work at pH = 4.0), working under a broad range of temperatures (22–42 °C), and a capability of transforming ZEA at high concentrations (up to 200 µg/mL). In addition, 23 Bacillus strains of various species were tested for their ZEA phosphorylation activity. Thirteen of the Bacillus strains showed phosphorylation functionality at an efficacy of between 20.3% and 99.4% after 24 h incubation, suggesting the metabolism pathway is widely conserved in Bacillus spp. This study established a new transformation system for potential application of controlling ZEA although the metabolism and toxicity of ZEA-14-phosphate requires further investigation.

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