scholarly journals A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fabio Palumbo ◽  
Andrea Squartini ◽  
Gianni Barcaccia ◽  
Stefano Macolino ◽  
Cristina Pornaro ◽  
...  
Keyword(s):  
Plant Composition ◽  
Faecal Microbiota ◽  
Lactating Cows ◽  
Plant Parasite ◽  
Faecal Samples ◽  
Gut Symbionts ◽  
Forage Value ◽  
Natural Grassland ◽  
Grazing Livestock ◽  
Vegetative Season

AbstractDiet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms’ interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

scholarly journals Faecal Microbiota Analysis of Piglets During Lactation

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 762 ◽  
Author(s):  
Tanya L. Nowland ◽  
Valeria A. Torok ◽  
Wai Y. Low ◽  
Mary D. Barton ◽  
Kate J. Plush ◽  
...  
Keyword(s):  
Antimicrobial Use ◽  
Animal Disease ◽  
Faecal Microbiota ◽  
Alpha And Beta Diversity ◽  
Animal Disease Control ◽  
Potential Development ◽  
Faecal Samples ◽  
Effect Of Treatment ◽  
Global Concern ◽  
Faecal Microbiome

Antimicrobial use in animals and the potential development of antimicrobial resistance is a global concern. So, non-antimicrobial techniques for animal disease control are needed. This study aimed to determine whether neonatal ceftiofur (CF) treatment affects piglet faecal microbiomes and whether faecal microbiome transplantation (FMT) can correct it. Two focal piglets per sow were assigned to treatments as follows: cffresh (n = 6) received CF (3 mg/kg intramuscular) at 7 d and fresh FMT at 13 d; cffrozen (n = 7) received CF at 7 d and frozen FMT at 13 d; CF (n = 8) received CF at 7 d and no FMT; and no CF (n = 5) received no CF or FMT. DNA was extracted from faecal samples collected on days 7, 13, and 18 for 16S rRNA amplicon analysis. All faecal blends used for the FMT consisted of pooled donor pig faeces at 1:2 ratio with saline, delivered orally at 3 mL/kg. Alpha and beta diversity metrics increased with age (p < 0.05). However, no effect of antibiotic or FMT treatment was evident in 13 and 18 d old piglets (p > 0.05). Although no effect of treatment was observed, information regarding microbial membership during lactation was gained.

scholarly journals Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study

Gut ◽  
2018 ◽  
Vol 67 (12) ◽  
pp. 2107-2115 ◽  
Author(s):  
Sofie Ingdam Halkjær ◽  
Alice Højer Christensen ◽  
Bobby Zhao Sheng Lo ◽  
Patrick Denis Browne ◽  
Stig Günther ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Controlled Trial ◽  
Symptom Relief ◽  
Controlled Study ◽  
Faecal Microbiota ◽  
Double Blind ◽  
Double Blind Placebo ◽  
Faecal Microbiota Transplantation ◽  
Faecal Samples ◽  
Significant Difference

ObjectiveIBS is associated with an intestinal dysbiosis and faecal microbiota transplantation (FMT) has been hypothesised to have a positive effect in patients with IBS. We performed a randomised, double-blind placebo-controlled trial to investigate if FMT resulted in an altered gut microbiota and improvement in clinical outcome in patients with IBS.DesignWe performed this study in 52 adult patients with moderate-to-severe IBS. At the screening visit, clinical history and symptoms were assessed and faecal samples were collected. Patients were randomised to FMT or placebo capsules for 12 days and followed for 6 months. Study visits were performed at baseline, 1, 3 and 6 months, where patients were asked to register their symptoms using the IBS-severity scoring system (IBS-SSS) and IBS-specific quality of life (IBS-QoL). Prior to each visit, faecal samples were collected.ResultsA significant difference in improvement in IBS-SSS score was observed 3 months after treatment (p=0.012) favouring placebo. This was similar for IBS-QoL data after 3 months (p=0.003) favouring placebo. Patients receiving FMT capsules had an increase in faecal microbial biodiversity while placebos did not.ConclusionIn this randomised double-blinded placebo-controlled study, we found that FMT changed gut microbiota in patients with IBS. But patients in the placebo group experienced greater symptom relief compared with the FMT group after 3 months. Altering the gut microbiota is not enough to obtain clinical improvement in IBS. However, different study designs and larger studies are required to examine the role of FMT in IBS.Trial registration numberNCT02788071.

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study

2018 ◽  
Vol 9 (1) ◽  
pp. 21-34 ◽  
Author(s):  
K. Adamberg ◽  
K. Kolk ◽  
M. Jaagura ◽  
R. Vilu ◽  
S. Adamberg
Keyword(s):  
Illumina Miseq ◽  
Well Being ◽  
Isothermal Microcalorimetry ◽  
Faecal Microbiota ◽  
Bifidobacterium Adolescentis ◽  
Functional Changes ◽  
Dietary Fibres ◽  
Faecal Samples ◽  
The Impact

The metabolic activity of colon microbiota is specifically affected by fibres with various monomer compositions, degree of polymerisation and branching. The supply of a variety of dietary fibres assures the diversity of gut microbial communities considered important for the well-being of the host. The aim of this study was to compare the impact of different oligo- and polysaccharides (galacto- and fructooligosaccharides, resistant starch, levan, inulin, arabinogalactan, xylan, pectin and chitin), and a glycoprotein mucin on the growth and metabolism of faecal microbiota in vitro by using isothermal microcalorimetry (IMC). Faecal samples from healthy donors were incubated in a phosphate-buffered defined medium with or without supplementation of a single substrate. The generation of heat was followed on-line, microbiota composition (V3-V4 region of the 16S rRNA using Illumina MiSeq v2) and concentrations of metabolites (HPLC) were determined at the end of growth. The multiauxic power-time curves obtained were substrate-specific. More than 70% of all substrates except chitin were fermented by faecal microbiota with total heat generation of up to 8 J/ml. The final metabolite patterns were in accordance with the microbiota changes. For arabinogalactan, xylan and levan, the fibre-affected distribution of bacterial taxa showed clear similarities (e.g. increase of Bacteroides ovatus and decrease of Bifidobacterium adolescentis). The formation of propionic acid, an important colon metabolite, was enhanced by arabinogalactan, xylan and mucin but not by galacto- and fructooligosaccharides or inulin. Mucin fermentation resulted in acetate, propionate and butyrate production in ratios previously observed for faecal samples, indicating that mucins may serve as major substrates for colon microbial population. IMC combined with analytical methods was shown to be an effective method for screening the impact of specific dietary fibres on functional changes in faecal microbiota.

scholarly journals A randomised crossover study investigating the effects of galacto-oligosaccharides on the faecal microbiota in men and women over 50 years of age

2011 ◽  
Vol 107 (10) ◽  
pp. 1466-1475 ◽  
Author(s):  
Gemma E. Walton ◽  
Ellen G. H. M. van den Heuvel ◽  
Marit H. W. Kosters ◽  
Robert A. Rastall ◽  
Kieran M. Tuohy ◽  
...  
Keyword(s):  
Proximal Colon ◽  
Faecal Microbiota ◽  
Double Blind ◽  
Men And Women ◽  
Increased Risk ◽  
Faecal Samples ◽  
Risk Of Disease ◽  
Butyrate Production

Faecal microbial changes associated with ageing include reduced bifidobacteria numbers. These changes coincide with an increased risk of disease development. Prebiotics have been observed to increase bifidobacteria numbers within humans. The present study aimed to determine if prebiotic galacto-oligosaccharides (GOS) could benefit a population of men and women of 50 years and above, through modulation of faecal microbiota, fermentation characteristics and faecal water genotoxicity. A total of thirty-seven volunteers completed this randomised, double-blind, placebo-controlled crossover trial. The treatments – juice containing 4 g GOS and placebo – were consumed twice daily for 3 weeks, preceded by 3-week washout periods. To study the effect of GOS on different large bowel regions, three-stage continuous culture systems were conducted in parallel using faecal inocula from three volunteers. Faecal samples were microbially enumerated by quantitative PCR.In vivo, following GOS intervention, bifidobacteria were significantly more compared to post-placebo (P = 0·02). Accordingly, GOS supplementation had a bifidogenic effect in allin vitrosystem vessels. Furthermore, in vessel 1 (similar to the proximal colon), GOS fermentation led to more lactobacilli and increased butyrate. No changes in faecal water genotoxicity were observed. To conclude, GOS supplementation significantly increased bifidobacteria numbersin vivoandin vitro. Increased butyrate production and elevated bifidobacteria numbers may constitute beneficial modulation of the gut microbiota in a maturing population.

scholarly journals Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children

2009 ◽  
Vol 103 (3) ◽  
pp. 335-338 ◽  
Author(s):  
Ramadass Balamurugan ◽  
Gemlyn George ◽  
Jayakanthan Kabeerdoss ◽  
Jancy Hepsiba ◽  
Aarthy M. S. Chandragunasekaran ◽  
...  
Keyword(s):  
Normal Weight ◽  
Obese Children ◽  
Faecal Microbiota ◽  
Dietary Survey ◽  
Indian Children ◽  
Faecalibacterium Prausnitzii ◽  
Faecal Samples ◽  
Significant Difference ◽  
Diet Recall ◽  
Faecal Bacteria

Gut bacteria contribute to energy conservation in man through their ability to ferment unabsorbed carbohydrate. The present study examined the composition of predominant faecal microbiota in obese and non-obese children. The participants (n 28) aged 11–14 years provided fresh faecal samples and completed a dietary survey consisting of 24 h diet recall and a FFQ of commonly used foods taken over the previous 3 months. Faecal bacteria were quantitated by real-time PCR using primers targeted at 16S rDNA. Of the participants, fifteen (seven female) were obese, with median BMI-for-age at the 99th percentile (range 97 to>99) while thirteen participants (seven female) were normal weight, with median BMI-for age being at the 50th percentile (range 1–85). Consumption of energy, carbohydrates, fat and protein was not significantly different between the obese and non-obese participants. There was no significant difference between the two groups in faecal levels of Bacteroides–Prevotella, Bifidobacterium species, Lactobacillus acidophilus group or Eubacterium rectale. Levels of Faecalibacterium prausnitzii were significantly higher in obese children than in non-obese participants (P = 0·0253). We concluded that the finding of increased numbers of F. prausnitzii in the faeces of obese children in south India adds to the growing information on alterations in faecal microbiota in obesity.

scholarly journals Effects of enhanced insect feeding on the faecal microbiota and transcriptome of a family of captive common marmosets (Callithrix jacchus)

2021 ◽  
Author(s):  
Yumiko Yamazaki ◽  
Shigeharu Moriya ◽  
Shinpei Kawarai ◽  
Hidetoshi Morita ◽  
Takefumi Kikusui ◽  
...  
Keyword(s):  
Control Group ◽  
Faecal Microbiota ◽  
Insect Feeding ◽  
Natural Habitats ◽  
Common Marmosets ◽  
Linear Discriminant ◽  
Functional Correlation ◽  
Faecal Samples ◽  
In The Wild ◽  
Physiological Impact

Common marmosets have been widely used in biomedical research for years. Nutritional control is an important factor in managing their health, and insect intake would be beneficial for that purpose because common marmosets frequently feed on insects in natural habitats. Here, we examined the effect of enhanced insect feeding on the gut by analysing the faecal microbiota and transcripts of captive marmosets. A family consisting of six marmosets was divided into two groups. During the seven-day intervention period, one group (the insect feeding group, or Group IF) was fed one cricket and one giant mealworm per marmoset per day, while the other (the control group, or Group C) was not fed these insects. RNA was extracted from faecal samples to evaluate the ecology and transcripts of the microbiota, which were then compared among time points before (Pre), immediately after (Post), and two weeks after intervention (After) by total RNA sequencing. The gut microbiota of marmosets showed Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria as dominant phyla. Linear discriminant analysis showed differential characteristics of microbiota with and without insect feeding treatment. Further analysis of differentially expressed genes revealed increases and decreases in Bacteroidetes and Firmicutes, respectively, corresponding to the availability of insects under both Post and After conditions. Significant changes specific to insect feeding were also detected within the transcriptome, some of which were synchronized with the fluctuations in the microbiota, suggesting a functional correlation or interaction between the two. The rapid changes in the microbiota and transcripts may be deeply connected to the original microbiota community shaped by marmoset feeding ecology in the wild. The results were informative for identifying the physiological impact of insect feeding to produce a better food regimen and for detecting transcripts that are currently unidentifiable.

scholarly journals The Equine Faecal Microbiota Undergoes Step-wise Compositional Changes in Accordance With Increasing Levels of Domestication

2021 ◽  
Author(s):  
Katie Bull ◽  
Gareth Davies ◽  
Timothy Patrick Jenkins ◽  
Laura Elizabeth Peachey
Keyword(s):  
Adult Female ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Faecal Samples ◽  
High Incidence ◽  
Life Threatening ◽  
Group Variation ◽  
The Uk

Abstract BackgroundChanges to the gut microbiota are associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathology. Horses are a prime example of a species which suffers from a high incidence of (often life-threatening) GI diseases in domesticated environments. We aimed to indentify the gut microbial changes which occur due to domestication in horses by profiling the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of domestication.MethodsFaecal samples were collected from 29 adult female Exmoor ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions; thus controlling for age, gender and random effects between groups. Diet and medication were recorded and faecal samples taken to assess parasite infection. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene.ResultsDownstream biostatistical analysis indicated profound step-wise changes in global microbial community structure in the transition from Feral to Semi-Feral to Domesticated groups. A relatively high abundance of members of the phylum Proteobacteria and Tenericutes were associated with the Domesticated group; and higher levels of Methanobacteria were seen in the Feral group. The Semi-Feral group frequently had intermediate levels of these taxa; however, they also exhibited the greatest ‘within group’ variation in bacterial diversity and parasites burdens. Functional predictions revealed increased amino acid and lipid metabolism in the Domesticated group and increased energy metabolism in the Feral group; supporting a hypothesis that differences in diet was the key driver of gut microbial composition. ConclusionsIf assumed the Feral population has a more natural gut microbial phenotype, akin to that with which horses have evolved, these data can potentially be used to provide microbial signitures of balanced gut homeostasis in horses; which, in turn, will aid prevention of GI disease in domesticated horses.

scholarly journals Dietary resistant and butyrylated starches have different effects on the faecal bacterial flora of azoxymethane-treated rats

2011 ◽  
Vol 105 (10) ◽  
pp. 1480-1485 ◽  
Author(s):  
Guy C. J. Abell ◽  
Claus T. Christophersen ◽  
Alexandra L. McOrist ◽  
Julie M. Clarke
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Flora ◽  
Epidemiological Studies ◽  
Rrna Gene ◽  
Maize Starch ◽  
Faecal Microbiota ◽  
Faecal Samples ◽  
Gradient Gel Electrophoresis ◽  
High Amylose ◽  
Bowel Health

Epidemiological studies have suggested that dietary fibre lowers the risk of colorectal cancer, which may be due to increased butyrate production from colonic fermentation of a type of fibre, resistant starch (RS). The present study investigated the effects of dietary RS and butyrylated RS on the faecal microbiota of rats treated with azoxymethane. A total of four groups of nine rats were fed diets containing either standard maize starch (low-amylose maize starch (LAMS), low RS), LAMS with 3 % tributyrin (LAMST), cooked 10 % high-amylose maize starch (HAMS, high RS) or cooked 10 % butyrylated HAMS (HAMSB). Faecal samples were examined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. Multivariate analysis demonstrated no differences between faecal microbiota before treatment but revealed differences in DGGE patterns between diet groups, with the exception of the two low-RS groups (LAMS and LAMST). Subsequent analysis identified eleven DGGE bands contributing significantly to the differentiation between diets. These phylotypes belonged to Clostridiales (five),Lactobacillus(one) and Bacteroidetes (five) lineages. Rats fed HAMS had increased concentration of propionate in their distal colonic digesta and developed faecal populations containingRuminococcus bromii-like bacteria. HAMSB increased propionate and butyrate concentrations in distal colonic digesta and was associated with the appearance of two non-butyrate-producing bacteria,Lactobacillus gasseriandParabacteroides distasonis.In conclusion, supplementation with specific dietary RS leads to changes in faecal microbiota profiles that may be associated with improved bowel health.

scholarly journals The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1762
Author(s):  
Mathijs J. P. Theelen ◽  
Roosmarijn E. C. Luiken ◽  
Jaap A. Wagenaar ◽  
Marianne M. Sloet van Oldruitenborgh-Oosterbaan ◽  
John W. A. Rossen ◽  
...  
Keyword(s):  
Environmental Factors ◽  
The Netherlands ◽  
Alpha Diversity ◽  
Sampling Technique ◽  
Illumina Miseq ◽  
Microbiota Composition ◽  
Faecal Microbiota ◽  
Related Factors ◽  
Small Pilot Study ◽  
Faecal Samples

Several studies have described the faecal microbiota of horses and the factors that influence its composition, but the variation in results is substantial. This study aimed to investigate the microbiota composition in healthy equids in The Netherlands under standard housing and management conditions and to evaluate the effect of age, gender, horse type, diet, pasture access, the season of sampling and location on it. Spontaneously produced faecal samples were collected from the stall floor of 79 healthy horses and ponies at two farms. The validity of this sampling technique was evaluated in a small pilot study including five ponies showing that the microbiota composition of faecal samples collected up to 6 h after spontaneous defaecation was similar to that of the samples collected rectally. After DNA extraction, Illumina Miseq 16S rRNA sequencing was performed to determine microbiota composition. The effect of host and environmental factors on microbiota composition were determined using several techniques (NMDS, PERMANOVA, DESeq2). Bacteroidetes was the largest phylum found in the faecal microbiota (50.1%), followed by Firmicutes (28.4%). Alpha-diversity and richness decreased significantly with increasing age. Location, age, season, horse type and pasture access had a significant effect on beta-diversity. The current study provides important baseline information on variation in faecal microbiota in healthy horses and ponies under standard housing and management conditions. These results indicate that faecal microbiota composition is affected by several horse-related and environment-related factors, and these factors should be considered in future studies of the equine faecal microbiota.

scholarly journals Interactions between Teladorsagia circumcincta Infections and Microbial Composition of Sheep with or without Successful Monepantel Treatment—A Preliminary Study

Ruminants ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 31-45
Author(s):  
Craig A. Watkins ◽  
Dave J. Bartley ◽  
Burcu Gündüz Ergün ◽  
Büşra Yıldızhan ◽  
Tracy Ross-Watt ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Terminal Ileum ◽  
Anthelmintic Resistance ◽  
Economic Losses ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Teladorsagia Circumcincta ◽  
Faecal Samples ◽  
Resistant Strains ◽  
Preliminary Study

Nematodes are one of the main impactors on the health, welfare and productivity of farmed animals. Teladorsagia circumcincta are endemic throughout many sheep-producing countries, particularly in the northern hemisphere, and contribute to the pathology and economic losses seen on many farms. Control of these nematode infections is essential and heavily reliant on chemotherapy (anthelmintics), but this has been compromised by the development of anthelmintic resistance. In mammals, the composition of the intestinal microbiota has been shown to have a significant effect on overall health. The interactions between host, microbiota and pathogens are complex and influenced by numerous factors. In this study, comparisons between intestinal and faecal microbiota of sheep infected with sensitive or resistant strains of T. circumcincta, with or without monepantel administration were assessed. The findings from both faecal samples and terminal ileum mucosal scrapings showed clear differences between successfully treated animals and those sheep that were left untreated and/or those carrying resistant nematodes. Specifically, the potentially beneficial genus Bifidobacterium was identified as elevated in successfully treated animals. The detection of these and other biomarkers will provide the basis for new therapeutic reagents particularly relevant to the problems of emerging multidrug anthelmintic resistance.

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