scholarly journals Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Timothy P. Jenkins ◽  
David I. Pritchard ◽  
Radu Tanasescu ◽  
Gary Telford ◽  
Marina Papaiakovou ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Experimental Infection ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Placebo Treatment ◽  
Sequencing Data ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Necator Americanus ◽  
Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

scholarly journals Experimental infection with the hookworm, Necator americanus, promotes gut microbial diversity in human volunteers with relapsing multiple sclerosis

2020 ◽  
Author(s):  
Timothy Jenkins ◽  
David Pritchard ◽  
Radu Tanasescu ◽  
Gary Telford ◽  
Marina Paraiakovou ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Gut Microbiota ◽  
Experimental Infection ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Placebo Treatment ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Necator Americanus ◽  
Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been recently linked to alterations of gut microbial communities. Results In the present study we investigated, for the first time, qualitative and quantitative changes in gut microbial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus ( N+ ), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment ( PBO ). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased microbial alpha diversity in the gut microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the gut microbiota of N + individuals for which no relapses were recorded at the end of the trial. Conclusions Overall, these data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immunomodulatory properties of hookworm parasites.

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 The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12562
Author(s):  
Zhiyuan Lu ◽  
Sisi Li ◽  
Hongxia Li ◽  
Zhucheng Wang ◽  
Derong Meng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Health It ◽  
Great Bustard ◽  
Microbial Composition ◽  
Protective Measures ◽  
Essential Information ◽  
Evaluation Indicator

Background The composition of the intestinal microbiota plays a significant role in modulating host health. It serves as a sensitive evaluation indicator and has substantial implications in protecting endangered species. Great Bustards are typical farmland-dependent wintering birds that are highly susceptible to the interference of human activities. However, information regarding their gut microbiota remains scarce. Methods To ensure a comprehensive analysis of this crucial data, we collected fecal samples from wild Great Bustards at their wintering habitat for two consecutive years. High-throughput sequencing of the 16S rRNA gene was subsequently applied to characterize their core gut microbiota and determine whether the gut microbial composition was similar or varied interannually. Results The gut microbiota of the Great Bustard was primarily comprised of four phyla: Firmicutes (82.87%), Bacteroidetes (7.98%), Proteobacteria (4.49%), and Actinobacteria (3.67%), accounting for 99.01% of the microbial community in all samples. Further analysis revealed 22 genera of core microbes and several pathogens. Notably, there were no significant differences in the alpha-diversity and beta-diversity between the two sample groups from different years. Conclusions This study provides essential information for assessing the health and developing targeted protective measures of this threatened species.

scholarly journals Xingnaojing injection can regulate dysbacteriosis and increase the concentration of short chain fatty acids in the feces after stroke in mice

2020 ◽  
Author(s):  
Jingfeng Lin ◽  
Ganlu Liu ◽  
Zhenyun Han ◽  
Qiang Gao ◽  
Zhenyi Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Enrichment Analysis ◽  
Illumina Miseq ◽  
Short Chain Fatty Acids ◽  
Normal Group ◽  
Sequencing Data ◽  
Germ Free ◽  
Xingnaojing Injection

AbstractBackgroundXingnaojing injection (XNJ) is extracted from the Chinese ancient prescription “An-Gong-Niu-Huang Pill”, is widely used for stroke in China. We mainly observe the effect of XNJ (Xingnaojing) injection on the gut microbiota in stroke model mice.MethodsForty-two 7-to 8-week-old male C57 mice weighing 22-24 g were chosen for the experiment. There were 6 mice in each group; the 7 groups were the normal group (NG), the MCAO group (CG), the MCAO+XNJ group (EG), the sham surgery group (SG), the sham germ-free normal group (SGFNG), the sham germ-free+MCAO group (SGFCG), and the sham germ-free+MCAO+XNJ group (SGFEG). Two days before modeling, we abdominally administered Xingnaojing (6 mg/kg) the SGFEG and EG groups. The processing time of sustained XNJ was 5 days. Three days after modeling, 1 ~ 2 mouse feces were collected, and after a MiSeq PE library was constructed, an Illumina MiSeq PE 300 platform was used for high-throughput sequencing. After cleaning the sequencing data, the microbiome and microbiomeseq packages were used for analysis using R software (version 3.6.2).ResultsAlpha diversity analysis revealed that the diversity was not different between the CG and EG. The Simpson index was different between the SGFCG and SGFEG. XNJ increased the levels of Sutterellaceae and decreased the level of Deferribacteres and Morganella. LEfSe analysis showed that SGFCG mice were also enriched with Morganella. XNJ increased the concentrations of the SCFAs PA (propionate), VA (valerate), IBA (isobutyrate), and IVA (isovalerate) in the feces of the SGFEG group. BA (butyrate) had greater positive correlation with gut bacteria than other acids in the SGFCG, and XNJ changed this trend. KEGG analysis showed that peptidoglycan biosynthesis was most different between the CG and EG.ConclusionIschemic stroke (IS) causes dysbiosis of some specific bacteria in the gut microbiota in MCAO mice. Xingnaojing ameliorated this condition by increasing the levels of Sutterellaceae and decreasing the level of Deferribacteres and Morganella. These results are in accordance with other research on Chinese medicines for IS that affect the gut microbiota. Enrichment analysis of SCFAs revealed that XNJ improved the levels of SCFAs through an energy metabolism-related pathway.

scholarly journals Effects of aging on the skin and gill microbiota of farmed seabass and seabream

2021 ◽  
Author(s):  
Daniela Rosado ◽  
Marcos Pérez-Losada ◽  
Ana Pereira ◽  
Ricardo Severino ◽  
Raquel Xavier
Keyword(s):  
Sexual Maturation ◽  
Metabolic Pathways ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Age Groups ◽  
Somatic Growth ◽  
Alpha Diversity ◽  
Microbial Composition ◽  
Effects Of Aging ◽  
The Impact

Abstract Background: Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. Results: Microbial diversity, composition and predicted metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha-diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota was significantly distinct from the fish microbiota across all the studied age groups, although a high percentage of ASVs was shared with the skin and gill microbiotas.Conclusions: We report important microbial differences in composition and potential functionality across different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the fish coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the microbiota of the fish external mucosae and highlight the importance of considering different life stages in microbiota studies.

scholarly journals Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome

2020 ◽  
pp. 1-14
Author(s):  
S. Holster ◽  
D. Repsilber ◽  
D. Geng ◽  
T. Hyötyläinen ◽  
A. Salonen ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Faecal Material ◽  
16S Rna ◽  
Irritable Bowel ◽  
Functional Profiles

Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of a patient with the aim to restore a disturbed gut microbiota. In this study, it was investigated whether FMT has an effect on faecal microbial composition, its functional capacity, faecal metabolite profiles and their interactions in 16 irritable bowel syndrome (IBS) patients. Faecal samples from eight different time points before and until six months after allogenic FMT (faecal material from a healthy donor) as well as autologous FMT (own faecal material) were analysed by 16S RNA gene amplicon sequencing and gas chromatography coupled to mass spectrometry (GS-MS). The results showed that the allogenic FMT resulted in alterations in the microbial composition that were detectable up to six months, whereas after autologous FMT this was not the case. Similar results were found for the functional profiles, which were predicted from the phylogenetic sequencing data. While both allogenic FMT as well as autologous FMT did not have an effect on the faecal metabolites measured in this study, correlations between the microbial composition and the metabolites showed that the microbe-metabolite interactions seemed to be disrupted after allogenic FMT compared to autologous FMT. This shows that FMT can lead to altered interactions between the gut microbiota and its metabolites in IBS patients. Further research should investigate if and how this affects efficacy of FMT treatments.

scholarly journals Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Huang ◽  
Han-Cheng Wang ◽  
Liu-Ti Cai ◽  
Wenhong Li ◽  
Daiwei Pan ◽  
...  
Keyword(s):  
Disease Severity ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Alpha Diversity ◽  
Disease Index ◽  
Microbial Composition ◽  
Tobacco Leaves ◽  
Tobacco Leaf ◽  
Bacterial Phyla

A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.

scholarly journals Effects of steam-flaked grains on foals’ growth and faecal microbiota

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Xiao Bin Li ◽  
Xin Xin Huang ◽  
Chang Jiang Zang ◽  
Chen Ma ◽  
Kai Xu Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Growth Performance ◽  
Relative Abundance ◽  
Alpha Diversity ◽  
The Body ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Faecal Samples ◽  
Health And Development

Abstract Background There is little objective information concerning the effect of steam-flaked grains on foal’s growth performance and faecal microbiota. To determine the effects of steam-flaked grains on foal’s growth performance and faecal microbiota, faecal samples were collection from 18 foals which had been fed either corn, oat or barley diets over the 60 days of the experiment. Body weight and conformation measurements were collected. Next-generation sequencing of the V3 + V4 region of the 16 S rRNA gene was used to assess the microbial composition of faeces. Alpha diversity, Venn graph, Relative abundance and beta diversity are presented. Results There was a significantly higher larger increase in the body weight of those foals fed barley compared to either corn or oats. There were also significant changes in the Alpha diversity of the gut microbiota. The Shannon and Simpson indices were significantly higher in the barley fed group than those fed corn or oats. The Chao1 index was significantly higher in the oat fed group than the corn or barley fed groups. There were significant changes in the relative abundance of bacteria in the microbiota in terms of phylum, family and genus. The histogram of LDA value distribution showed that the 12 statistically different biomarkers of the bacteria were present. Tax4Fun function annotation clustering heat map showed that functional information was detected from 26 species of bacteria in faecal samples from the foals. Conclusions Differences by starch sources were found in overall growth of the foals and in the faecal microbiota if either supplementary corn, oat or barley was fed. Further studies are required to determine the potential impact of the changes in the microbiota on the health and development of foals fed cereal starch of different sources.

scholarly journals Effects of Steam-Flaked Grains On Foals Growth Performance And Faecal Microbiota

2021 ◽  
Author(s):  
XiaoBin Li ◽  
Xin Xin Huang ◽  
Chang Jiang Zang ◽  
Chen Ma ◽  
Kai Xu Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Weight Gain ◽  
Growth Performance ◽  
Relative Abundance ◽  
Alpha Diversity ◽  
The Body ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Microbial Composition

Abstract BackgroundThere is little objective information concerning the effect of steam-flaked grains on foal’s growth performance and faecal microbiota.To determine the effects of steam-flaked grains on foal’s growth performance and faecal microbiota.Faecal samples were collection from 18 foals which had been fed corn, oat or barley diets over the 60 days of the experiment. Body weight and measurements were collected. Next-generation sequencing of the V3+V4 region of the 16S rRNA gene was used to assess the microbial composition of faeces. Alpha diversity, Venn graph, Relative abundance and beta diversity are presented.ResultsThere was a significantly higher increase in the body weight of those foals fed barley compared to either corn or oats, both in terms of the total weight gain and the daily weight gain (P=0.0185). There were also significant changes in the Alpha diversity. The Shannon and Simpson indices were higher in the barley fed group than those fed corn or oats (P<0.05, P<0.05, P<0.05 and P<0.05). The Chao1 index was higher in the oat fed group than the corn or barley fed groups (P<0.05 and P<0.05). There were significant changes in the relative abundance of bacteria in the microbiota in terms of phylum, family and genus. The histogram of LDA value distribution showed that the statistically different biomarkers of the bacteria was 12. Tax4Fun function annotation clustering heat map showed that functional information was detected from 26 species of bacteria in faecal samples from the foals.ConclusionsDifferences were seen in the faecal microbiota of foals fed either corn, oat or barley, and also differences in the overall growth of the foals. Different grains have different impact on faecal microbiota, which are mainly related to the grain sources. Further investigation is required to look at the potential impact of changes in the microbiota on the functional impact on foals when fed grains.

scholarly journals Effects of aging on the skin and gill microbiota of farmed seabass and seabream

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Marcos Pérez-Losada ◽  
Ana Pereira ◽  
Ricardo Severino ◽  
Raquel Xavier
Keyword(s):  
Sexual Maturation ◽  
Metabolic Pathways ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Age Groups ◽  
Somatic Growth ◽  
Alpha Diversity ◽  
Microbial Composition ◽  
Effects Of Aging ◽  
The Impact

Abstract Background Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. Results Microbial diversity, composition and predicted metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha-diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota was significantly distinct from the fish microbiota across all the studied age groups, although a high percentage of ASVs was shared with the skin and gill microbiotas. Conclusions We report important microbial differences in composition and potential functionality across different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the fish coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the microbiota of the fish external mucosae and highlight the importance of considering different life stages in microbiota studies.

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