scholarly journals Lactulose drives a reversible reduction and qualitative modulation of the faecal microbiota diversity in healthy dogs

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Marisa da Fonseca Ferreira ◽  
Silke Salavati Schmitz ◽  
Jeffrey Joseph Schoenebeck ◽  
Dylan Neil Clements ◽  
Susan Mary Campbell ◽  
...  
Keyword(s):  
Hepatic Encephalopathy ◽  
16S Rrna Gene Sequencing ◽  
Large Animal Model ◽  
Rrna Gene ◽  
Large Animal ◽  
Faecal Microbiota ◽  
Operational Taxonomic Units ◽  
Faecal Samples ◽  
Rrna Gene Sequencing ◽  
Privately Owned

Abstract Hepatic encephalopathy is a frequent and debilitating complication of liver disorders. Lactulose is an established and reasonably effective treatment, yet with incompletely understood mechanisms of action. The aims of this study were to examine how the faecal microbiota composition changed before, during and after lactulose treatment in a large animal model. Healthy, privately owned dogs (n = 18) completed a prospective cohort study. Faecal samples were collected weekly, while the subjects were either on their usual diet (week 1), or a standardised diet (weeks 2–9), with added oral lactulose in weeks 6–7. DNA extraction and 16S rRNA gene sequencing were undertaken. Faecal samples from week 7 had a significantly lower microbiota richness/diversity, based on observed operational taxonomic units, Shannon/Chao1 indexes and Pielou’s Evenness. Beta diversity based on UniFrac distances was significantly different in week 7 compared to weeks 1, 5 and 9. At the phylum level, week 7 was associated with a significant increase of Firmicutes and Actinobacteria, and a decrease of Bacteroidetes and Fusobacteria, when compared to weeks 5 and 9. In summary, we have shown that lactulose induces a reversible qualitative and quantitative change of the faecal microbiota, which may explain its clinical efficacy in the management of hepatic encephalopathy.

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.

scholarly journals Streptococcus australis and Ralstonia pickettii as Major Microbiota in Mesotheliomas

2021 ◽  
Vol 11 (4) ◽  
pp. 297
Author(s):  
Rumi Higuchi ◽  
Taichiro Goto ◽  
Yosuke Hirotsu ◽  
Sotaro Otake ◽  
Toshio Oyama ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Pcr Amplification ◽  
16S Rrna Gene Sequencing ◽  
Abundant Species ◽  
Rrna Gene ◽  
Tissue Samples ◽  
Ralstonia Pickettii ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing ◽  
Almost All

The microbiota has been reported to be correlated with carcinogenesis and cancer progression. However, its involvement in the pathology of mesothelioma remains unknown. In this study, we aimed to identify mesothelioma-specific microbiota using resected or biopsied mesothelioma samples. Eight mesothelioma tissue samples were analyzed via polymerase chain reaction (PCR) amplification and 16S rRNA gene sequencing. The operational taxonomic units (OTUs) of the effective tags were analyzed in order to determine the taxon composition of each sample. For the three patients who underwent extra pleural pneumonectomy, normal peripheral lung tissues adjacent to the tumor were also included, and the same analysis was performed. In total, 61 OTUs were identified in the tumor and lung tissues, which were classified into 36 species. Streptococcus australis and Ralstonia pickettii were identified as abundant species in almost all tumor and lung samples. Streptococcus australis and Ralstonia pickettii were found to comprise mesothelioma-specific microbiota involved in tumor progression; thus, they could serve as targets for the prevention of mesothelioma.

scholarly journals Bacterial Communities Associated with the Cycling of Non-Starch Polysaccharides and Phytate in Aquaponics Systems

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 631
Author(s):  
Daniel Menezes-Blackburn ◽  
Nahad Al-Mahrouqi ◽  
Buthaina Al-Siyabi ◽  
Adhari Al-Kalbani ◽  
Ralf Greiner ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Pcr Amplification ◽  
Aquatic Organisms ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Culture Techniques ◽  
Operational Taxonomic Units ◽  
Catalytic Mechanisms ◽  
Rrna Gene Sequencing

Aquaponics are efficient systems that associate aquatic organisms’ production and plants by recirculating water and nutrients between aquaculture and hydroponic tanks. In this study, we characterised the bacterial communities in the freshwater aquaponics system that can mineralise polysaccharides and phytate by producing carbohydrate-degrading enzymes and phytases, by 16S rRNA gene sequencing and in vitro culture techniques. Around 20% of the operational taxonomic units (zOTUs) identified were previously reported to carry fibre-degrading enzyme putative genes, namely β-glucanase (1%), xylanase (5%), or cellulases (17%). Ten % of the zOTUs were previously reported to carry putative genes of phytases with different catalytic mechanisms, namely β-propeller (6%), histidine acid phytases (3%), and protein tyrosine phytase (<1%). Thirty-eight morphologically different bacteria were isolated from biofilms accumulated in fish and plant compartments, and identified to belong to the Bacilli class. Among these, 7 could produce xylanase, 8 produced β-glucanase, 14 produced cellulase, and 11 isolates could secrete amylases. In addition, Staphylococcus sp. and Rossellomorea sp. could produce consistent extracellular phytate-degrading activity. The PCR amplification of β-propeller genes both in environmental samples and in the isolates obtained showed that this is the most ecologically relevant phytase type in the aquaponics systems used. In summary, the aquaponics system is abundant with bacteria carrying enzymes responsible for plant-nutrient mineralisation.

scholarly journals Effects of obesity, energy restriction and neutering on the faecal microbiota of cats

2017 ◽  
Vol 118 (7) ◽  
pp. 513-524 ◽  
Author(s):  
Manuela M. Fischer ◽  
Alexandre M. Kessler ◽  
Dorothy A. Kieffer ◽  
Trina A. Knotts ◽  
Kyoungmi Kim ◽  
...  
Keyword(s):  
Weight Loss ◽  
Intestinal Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Energy Restriction ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Bacterial Populations ◽  
Before And After ◽  
Rrna Gene Sequencing ◽  
New Strategies

AbstractSurveys report that 25–57 % of cats are overweight or obese. The most evinced cause is neutering. Weight loss often fails; thus, new strategies are needed. Obesity has been associated with altered gut bacterial populations and increases in microbial dietary energy extraction, body weight and adiposity. This study aimed to determine whether alterations in intestinal bacteria were associated with obesity, energy restriction and neutering by characterising faecal microbiota using 16S rRNA gene sequencing in eight lean intact, eight lean neutered and eight obese neutered cats before and after 6 weeks of energy restriction. Lean neutered cats had a bacterial profile similar to obese rodents and humans, with a greater abundance (P<0·05) of Firmicutes and lower abundance (P<0·05) of Bacteroidetes compared with the other groups. The greater abundance of Firmicutes in lean neutered cats was due to a bloom in Peptostreptococcaceae. Obese cats had an 18 % reduction in fat mass after energy restriction (P<0·05). Energy reduction was concurrent with significant shifts in two low-abundance bacterial genera and trends in four additional genera. The greatest change was a reduction in the Firmicutes genus,Sarcina, from 4·54 to 0·65 % abundance after energy restriction. The short duration of energy restriction may explain why few bacterial changes were observed in the obese cats. Additional work is needed to understand how neutering, obesity and weight loss are related to changes in feline microbiota and how these microbial shifts affect host physiology.

scholarly journals Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3167
Author(s):  
Zhimin Zhang ◽  
Li Yang ◽  
Yang He ◽  
Xinmao Luo ◽  
Shaokang Zhao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Similar Species ◽  
Operational Taxonomic Units ◽  
Angus Cattle ◽  
Fecal Bacterial Community ◽  
The Difference ◽  
Rrna Gene Sequencing

This study is to investigate the difference in bovine fecal microbiota between grazing and feedlot Angus cattle. Fecal samples were collected from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene. Sequencing of the V3–V4 region totally produced 1,113,170 effective tages that were computationally clustered into 775 operational taxonomic units (OTUs). These 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species. The dominant phyla were Firmicutes and Bacteroidetes. There was similar species richness between grazing and feedlot Angus beef, while higher species diversity was observed in feedlot Angus beef. The relative abundance of Firmicutes, Cyanobacteria, Elusimicrobia and Patescibacteria was significantly different between grazing and feedlot Angus beef (p < 0.05). At a genus level, five microbiotas were significantly different between the two groups and all belonged to the Firmicutes phylum. These significant differences in microbiota composition between grazing and feedlot Angus beef may have an impact on the meat quality of Angus beef.

scholarly journals A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

2016 ◽  
Author(s):  
Matthew A Jackson ◽  
Jordana T Bell ◽  
Tim D Spector ◽  
Claire J Steves
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
De Novo ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Clustering Methods ◽  
Taxonomic Assignment ◽  
Biologically Relevant ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.

scholarly journals No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population

Gut ◽  
2019 ◽  
Vol 69 (6) ◽  
pp. 1076-1084 ◽  
Author(s):  
Luisa W Hugerth ◽  
Anna Andreasson ◽  
Nicholas J Talley ◽  
Anna M Forsberg ◽  
Lars Kjellström ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Self Rated Health ◽  
Faecal Samples ◽  
Rrna Gene Sequencing ◽  
Irritable Bowel ◽  
Taxonomic Groups ◽  
Faecal Microbiome

ObjectiveThe ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings.DesignThe PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases).ResultsWhile sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R²=0.255, p<3E-11) as was diversity (R²=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson’s r=−0.1, p=0.08) and poorer self-rated health (r=−0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=−0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=−0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals.ConclusionsNo distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.

scholarly journals Influence of Enteral Nutrition on Gut Microbiota Composition in Patients with Crohn’s Disease: A Systematic Review

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2551 ◽  
Author(s):  
Paulina Horwat ◽  
Stanisław Kopeć ◽  
Aleksandra Garczyk ◽  
Iwona Kaliciak ◽  
Zuzanna Staręga ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Enteral Nutrition ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Exclusive Enteral Nutrition ◽  
Faecal Samples ◽  
Hs Crp ◽  
Rrna Gene Sequencing

The aim of the study was to systematically and comprehensively evaluate whether exclusive enteral nutrition (EEN) has impact on gut microbiota in patients with Crohn’s disease (CD). The databases PUBMED (MEDLINE), SCOPUS and WEB OF SCIENCE were searched. Out of 232 studies, 9 met inclusion criteria. The combined analyzed population consists of 118 patients with CD and treated with EEN with a time of intervention of 2–12 weeks. Studies were conducted in children, with the exception of one study. All applied feeding formulas had similar energy value and composition. The microbiome analysis was based on 16S rRNA gene sequencing of faecal samples. In all studies, EEN treatment decreases inflammatory markers (i.e., hs-CRP and FCP). A change in abundance of numerous bacterial families (Clostridiaceae, Eubacteriaceae, Bacteroidaceae) was noticed, especially in Bacteroidaceae. An increase in families connected to the more severe clinical course (Fusobacteria, Prevotella, Lachnospiraceae) was observed in only 2.5% of CD patients. Our analyses suggest EEN has a beneficial influence on gut microbiome in patients with CD, which is interrelated with clinical patient’s improvement and time of disease remission.

scholarly journals A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

2016 ◽  
Author(s):  
Matthew A Jackson ◽  
Jordana T Bell ◽  
Tim D Spector ◽  
Claire J Steves
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
De Novo ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Clustering Methods ◽  
Taxonomic Assignment ◽  
Biologically Relevant ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.

scholarly journals Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice

2019 ◽  
Vol 317 (5) ◽  
pp. G618-G624 ◽  
Author(s):  
Fang Zhou ◽  
Henry A. Paz ◽  
Mahrou Sadri ◽  
Juan Cui ◽  
Stephen D. Kachman ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bovine Milk ◽  
Cell Communication ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Rrna Gene Sequencing

Exosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant, and bacteria. Dietary exosomes in bovine milk are bioavailable in nonbovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA-depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age 3 wk, and cecum content was collected at ages 7, 15, and 47 wk. Microbial communities were identified by 16S rRNA gene sequencing. Milk exosomes altered bacterial communities in the murine cecum. The abundance of three phyla, seven families, and 52 operational taxonomic units (OTUs) was different in the ceca from mice fed ERD and ERS ( P < 0.05). For example, at the phylum level, Tenericutes had more than threefold abundance in ERS mice at ages 15 and 47 wk compared with ERD mice ( P < 0.05). At the family level, Verrucomicrobiaceae were much less abundant in ERS mice compared with ERD mice age 47 wk ( P < 0.05). At the OTU level, four OTUs from the family of Lachnospiraceae were more than two times more abundant in ERS mice compared with ERD at age 7 and 47 wk ( P < 0.05). We conclude that exosomes in bovine milk alter microbial communities in nonbovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms. NEW & NOTEWORTHY This is the first report that exosomes from bovine milk alter microbial communities in mice. This report suggests that the gut microbiome facilitates cell-to-cell communication by milk exosomes across species boundaries, and milk exosomes facilitate communication across animal and bacteria kingdoms.

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