Diets supplemented with chickpea or its main oligosaccharide component raffinose modify faecal microbial composition in healthy adults

2010 ◽  
Vol 1 (2) ◽  
pp. 197-207 ◽  
Author(s):  
W. Fernando ◽  
J. Hill ◽  
G. Zello ◽  
R. Tyler ◽  
W. Dahl ◽  
...  
Keyword(s):  
16S Rrna ◽  
Pathogenic Bacteria ◽  
Control Diet ◽  
Rflp Analysis ◽  
Healthy Adults ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Clone Libraries ◽  
Bacterial Populations ◽  
Significant Difference

The effects of diets supplemented with either chickpea or its main oligosaccharide raffinose on the composition of the faecal microbial community were examined in 12 healthy adults (18-65 years) in a randomised crossover intervention study. Subjects consumed their usual diet supplemented with soups and desserts that were unfortified, or fortified with either 200 g/d of canned chickpeas or 5 g/d of raffinose for 3 week periods. Changes in faecal bacterial populations of subjects were examined using 16S rRNA-based terminal restriction fragment length polymorphisms (T-RFLP) and clone libraries generated from the diet pools. Classification of the clone libraries and T-RFLP analysis revealed that Faecalibacterium prausnitzii, reported to be an efficient butyrate producer and a highly metabolically active bacterium in the human intestinal microbiota, was more abundant in the raffinose diet and the chickpea diet compared to the control diet. However, no significant difference was observed in the faecal total short chain fatty acid concentration or in the levels of the components (butyrate, acetate and propionate) with the chickpea diet or the raffinose diet compared to the control diet. Bifidobacterium species were detected by T-RFLP in all three diet groups and quantitative real-time PCR (qPCR) analysis showed a marginal increase in 16S rRNA gene copies of Bifidobacterium with the raffinose diet compared to control (P>0.05). The number of individuals showing TRFs for the Clostridium histolyticum - Clostridum lituseburense groups, which include pathogenic bacteria species and putrefactive bacteria, were lower in the chickpea diet compared to the other two treatments. Diet appeared to affect colonisation by a high ammonia-producing bacterial isolate which was detected in 83%, 92% and 42% of individuals in the control, raffinose and chickpea groups, respectively. Our results indicate that chickpea and raffinose have the potential to modulate the intestinal microbial composition to promote intestinal health in humans.

scholarly journals Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Susan W. Muriuki ◽  
Michael S. Rengan ◽  
Nancy L. M. Budambula
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Samples ◽  
Pathogenic Bacteria ◽  
Risk Group ◽  
Foodborne Diseases ◽  
Rrna Gene ◽  
Prokaryotic Diversity ◽  
Hygiene Measures ◽  
Significant Difference

Abstract Purpose Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market. Methods The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3. Results Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1). Conclusion The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.

scholarly journals Community Structure and Diversity of Biofilms from a Beer Bottling Plant as Revealed Using 16S rRNA Gene Clone Libraries

2005 ◽  
Vol 71 (10) ◽  
pp. 6446-6452 ◽  
Author(s):  
Markus Timke ◽  
Ngoc Quynh Wang-Lieu ◽  
Karlheinz Altendorf ◽  
André Lipski
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
Fatty Acid Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Microbial Composition ◽  
Clone Libraries

ABSTRACT The microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16S rRNA genes. Clone libraries were differentiated by amplified 16S rRNA gene restriction analysis and representative clones from each group were sequenced. The diversity of the clone libraries was comparable with the diversity found for environmental samples. No evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that biofilms developed for more than 6 months at the plant formed no appropriate habitat for those microorganisms. The genus Methylobacterium was one of the dominating groups of the clone libraries. The size of this population was assessed by fluorescence in situ hybridization and fatty acid analysis. In addition, considerable numbers of clones were assigned to uncultivated organisms.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

scholarly journals Molecular Detection and Phylogeny of Anaplasmaphagocytophilum and Related Variants in Small Ruminants from Turkey

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 814
Author(s):  
Münir Aktaş ◽  
Sezayi Özübek ◽  
Mehmet Can Uluçeşme
Keyword(s):  
16S Rrna ◽  
Small Ruminants ◽  
Rrna Gene ◽  
Infection Rates ◽  
Sheep And Goats ◽  
Significant Difference ◽  
Pcr Rflp ◽  
First Time ◽  
Japan And China ◽  
Apparently Healthy

Anaplasma phagocytophilum causes tick-borne fever in small ruminants. Recently, novel Anaplasma variants related to A. phagocytophilum have been reported in ruminants from Tunisia, Italy, South Korea, Japan, and China. Based on 16S rRNA and groEL genes and sequencing, we screened the frequency of A. phagocytophilum and related variants in 433 apparently healthy small ruminants in Turkey. Anaplasma spp. overall infection rates were 27.9% (121/433 analyzed samples). The frequency of A. phagocytophilum and A. phagocytophilum-like 1 infections was 1.4% and 26.5%, respectively. No A. phagocytophilum-like 2 was detected in the tested animals. The prevalence of Anaplasma spp. was comparable in species, and no significant difference was detected between sheep and goats, whereas the prevalence significantly increased with tick infestation. Sequencing confirmed PCR-RFLP data and showed the presence of A. phagocytophilum and A. phagocytophilum-like-1 variant in the sampled animals. Phylogeny-based on 16S rRNA gene revealed the A. phagocytophilum-like 1 in a separate clade together with the previous isolates detected in small ruminants and ticks. In this work, A. phagocytophilum-like 1 has been detected for the first time in sheep and goats from Turkey. This finding revealed that the variant should be considered in the diagnosis of caprine and ovine anaplasmosis.

scholarly journals Anaplasma Infection in Ticks in Southeastern Region of Iran

2020 ◽  
Author(s):  
Reza Ranjbar ◽  
Mehdi Anjomruz ◽  
Ahmad Ali Enayati ◽  
Mehdi Khoobdel ◽  
Atiyeh Rafinejad ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cold Chain ◽  
Rrna Gene ◽  
Infection Rates ◽  
Male And Female ◽  
Significant Difference ◽  
High Infection ◽  
Hyalomma Marginatum ◽  
Southeastern Region

Background: Anaplasmosis and Ehrlichiosis are the most important tick-borne diseases. This study was conducted in three cities of Kerman Province in Iran to investigate the circulation of the bacteria in ticks collected from sheep. Methods: Ticks were collected from animals using Srkj forceps and transferred to the Entomology lab in cold chain. After specimen’s identification, they kept at -70 ºC. Tick DNA was extracted using Bioneers DNA extraction kits followed by Nested PCR technique to amplify ribosomal 16S rRNA gene to detect Anaplasma infection in ticks. Results: 472 sheep were examined from which 349 ticks were collected and identified in laboratory using valid keys. Tick specimens belonged to two genera and four species; Hyalomma marginatum (62.47%) was the most frequent and Hylomma asiaticum (5.73%) showed the least abundance. The infestation rate to different tick species was different in three regions of Kerman Province. Observation revealed that 24 specimens (58.3%) were positive for Anaplasma. There is a significant difference between male and female infection rate. However, there is no significant difference between these variables in each of these cities. Conclusion: This study shows high infection rates to Anaplasma in hard ticks. It is essential for health and veterinary authorities and farmers to use appropriate strategies to control ticks to reduce the infestation.

scholarly journals Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

2021 ◽  
Vol 11 ◽  
Author(s):  
Shiju Xiao ◽  
Guangzhong Zhang ◽  
Chunyan Jiang ◽  
Xin Liu ◽  
Xiaoxu Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Target Genes ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phosphotransferase System ◽  
Microbial Composition ◽  
Kegg Pathways ◽  
Significant Difference ◽  
Rrna Gene Sequencing ◽  
Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

scholarly journals Apis andreniformis associated Actinomycetes show antimicrobial activity against black rot pathogen (Xanthomonas campestris pv. campestris)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12097
Author(s):  
Yaowanoot Promnuan ◽  
Saran Promsai ◽  
Wasu Pathom-aree ◽  
Sujinan Meelai
Keyword(s):  
Antimicrobial Activity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Honey Bee ◽  
Pseudomonas Syringae ◽  
Xanthomonas Campestris ◽  
Pathogenic Bacteria ◽  
Rrna Gene ◽  
Apis Andreniformis

This study aimed to investigate cultivable actinomycetes associated with rare honey bee species in Thailand and their antagonistic activity against plant pathogenic bacteria. Actinomycetes were selectively isolated from the black dwarf honey bee (Apis andreniformis). A total of 64 actinomycete isolates were obtained with Streptomyces as the predominant genus (84.4%) followed by Micromonospora (7.8%), Nonomuraea (4.7%) and Actinomadura (3.1%). All isolates were screened for antimicrobial activity against Xanthomonas campestris pv. campestris, Pectobacterium carotovorum and Pseudomonas syringae pv. sesame. Three isolates inhibited the growth of X. campestris pv. campestris during in vitro screening. The crude extracts of two isolates (ASC3-2 and ASC5-7P) had a minimum inhibitory concentration (MIC) of 128 mg L−1against X. campestris pv. campestris. For isolate ACZ2-27, its crude extract showed stronger inhibitory effect with a lower MIC value of 64 mg L−1 against X. campestris pv. campestris. These three active isolates were identified as members of the genus Streptomyces based on their 16S rRNA gene sequences. Phylogenetic analysis based on the maximum likelihood algorithm showed that isolate ACZ2-27, ASC3-2 and ASC5-7P were closely related to Streptomyces misionensis NBRC 13063T (99.71%), Streptomyces cacaoi subsp. cacaoi NBRC 12748T (100%) and Streptomyces puniceus NBRC 12811T (100%), respectively. In addition, representative isolates from non-Streptomyces groups were identified by 16S rRNA gene sequence analysis. High similarities were found with members of the genera Actinomadura, Micromonospora and Nonomuraea. Our study provides evidence of actinomycetes associated with the black dwarf honey bee including members of rare genera. Antimicrobial potential of these insect associated Streptomyces was also demonstrated especially the antibacterial activity against phytopathogenic bacteria.

scholarly journals A novel subgroup 16SrVII-D phytoplasma identified in association with erigeron witches' broom

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2761-2765 ◽  
Author(s):  
Daniela Flôres ◽  
Ana Paula de Oliveira Amaral Mello ◽  
Thays Benites Camargo Pereira ◽  
Jorge Alberto Marques Rezende ◽  
Ivan Paulo Bedendo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Phytoplasma Strain ◽  
Total Dna ◽  
Virtual Rflp ◽  
The 16S Rrna Gene

Erigeron sp. plants showing symptoms of witches' broom and stunting were found near orchards of passion fruit in São Paulo state, Brazil. These symptoms were indicative of infection by phytoplasmas. Thus, the aim of this study was to detect and identify possible phytoplasmas associated with diseased plants. Total DNA was extracted from symptomatic and asymptomatic plants and used in nested PCR conducted with the primer pairs P1/Tint and R16F2n/16R2. Amplification of genomic fragments of 1.2 kb from the 16S rRNA gene confirmed the presence of phytoplasma in all symptomatic samples. The sequence identity scores between the 16S rRNA gene of the phytoplasma strain identified in the current study and those of previously reported ‘Candidatus Phytoplasma fraxini’-related strains ranged from 98 % to 99 % indicating the phytoplasma to be a strain affiliated with ‘Candidatus Phytoplasma fraxini’. The results from a phylogenetic analysis and virtual RFLP analysis of the 16S rRNA gene sequence with 17 restriction enzymes revealed that the phytoplasma strain belongs to the ash yellows phytoplasma group (16SrVII); the similarity coefficient of RFLP patterns further suggested that the phytoplasma represents a novel subgroup, designated 16SrVII-D. The representative of this new subgroup was named EboWB phytoplasma (Erigeron bonariensis Witches' Broom).

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