Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

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Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota

10.1101/313577 ◽

2018 ◽

Cited By ~ 1

Author(s):

Wei Yan ◽

Jiangxia Zheng ◽

Chaoliang Wen ◽

Congliang Ji ◽

Dexiang Zhang ◽

...

Keyword(s):

Small Intestine ◽

Community Structure ◽

Microbial Community ◽

Gut Microbiota ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Fecal Samples ◽

Community Membership ◽

16S Rrna Amplicon Sequencing ◽

Fecal Sampling

AbstractBackgroundDespite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum and feces samples, for 16S rRNA amplicon sequencing analyses.ResultsIn this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11 – 87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54 – 0.71 and 0.71 – 0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the 4 gut segments, and these correlations were not high (ρ = −0.2 – 0.4, P < 0.05) for most genera.ConclusionsOur results provide evidence that the good potential of feces to identify most taxa in chicken guts, but it should be interpreted with caution by using feces as a proxy for gut in microbial structure analyses. This work provides insights and future directions regarding the usage of fecal samples in studies of the gut microbiome.

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Pulmonary and intestinal microbiota dynamics during Gram-negative pneumonia-derived sepsis

Intensive Care Medicine Experimental ◽

10.1186/s40635-021-00398-4 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Nora S. Wolff ◽

Max C. Jacobs ◽

W. Joost Wiersinga ◽

Floor Hugenholtz

Keyword(s):

Gut Microbiota ◽

Pulmonary Inflammation ◽

Alpha Diversity ◽

Severe Pneumonia ◽

Fecal Microbiota ◽

Protective Role ◽

Oral Microbiota ◽

Post Inoculation ◽

Systemic Spread ◽

Pathogen Burden

Abstract Background The gut microbiome plays a protective role in the host defense against pneumonia. The composition of the lung microbiota has been shown to be predictive of clinical outcome in critically ill patients. However, the dynamics of the lung and gut microbiota composition over time during severe pneumonia remains ill defined. We used a mouse model of pneumonia-derived sepsis caused by Klebsiella pneumoniae in order to follow the pathogen burden as well as the composition of the lung, tongue and fecal microbiota from local infection towards systemic spread. Results Already at 6 h post-inoculation with K. pneumoniae, marked changes in the lung microbiota were seen. The alpha diversity of the lung microbiota did not change throughout the infection, whereas the beta diversity did. A shift between the prominent lung microbiota members of Streptococcus and Klebsiella was seen from 12 h onwards and was most pronounced at 18 h post-inoculation (PI) which was also reflected in the release of pro-inflammatory cytokines indicating severe pulmonary inflammation. Around 18 h PI, K. pneumoniae bacteremia was observed together with a systemic inflammatory response. The composition of the tongue microbiota was not affected during infection, even at 18–30 h PI when K. pneumoniae had become the dominant bacterium in the lung. Moreover, we observed differences in the gut microbiota during pulmonary infection. The gut microbiota contributed to the lung microbiota at 12 h PI, however, this decreased at a later stage of the infection. Conclusions At 18 h PI, K. pneumoniae was the dominant member in the lung microbiota. The lung microbiota profiles were significantly explained by the lung K. pneumoniae bacterial counts and Klebsiella and Streptococcus were correlating with the measured cytokine levels in the lung and/or blood. The oral microbiota in mice, however, was not influenced by the severity of murine pneumonia, whereas the gut microbiota was affected. This study is of significance for future studies investigating the role of the lung microbiota during pneumonia and sepsis.

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Straw-Based Biopurification Systems to Remove Ibuprofen, Diclofenac and Triclosan from Wastewaters: Dominant Microbial Communities

Agronomy ◽

10.3390/agronomy11081507 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1507

Author(s):

Laura Delgado-Moreno ◽

Pieter van Dillewijn ◽

Rogelio Nogales ◽

Esperanza Romero

Keyword(s):

Community Structure ◽

Microbial Community ◽

Point Source ◽

Relative Abundance ◽

Alpha Diversity ◽

Microbial Structure ◽

Methyl Triclosan ◽

Source Contamination ◽

Biopurification Systems ◽

Olive Mill

The continued discharge of pharmaceuticals and personal care products (PPCPs) into the environment due to their widespread use and the lack of effective systems for their removal from water is a global problem. In this study, the dissipation of ibuprofen, diclofenac and triclosan added simultaneously in biopurification systems (BPSs) with different compositions and their effect on the microbial community structure was analysed. Three BPSs, constituted by mixtures of soil (S), peat (P), or raw wet olive mill cake (A) or its vermicompost (V) and straw (S) were prepared (SPS, SAS and SVS). Sorption and degradation experiments were carried out. After 84 days of incubation, more than 85% of each PPCP applied had dissipated. Methyl-triclosan was determined to be highest in the SVS biomixture. Biomixtures with lower C/N ratio and higher alpha diversity were the most effective in the removal of PPCPs. Initially, the BPS biomixtures showed a different microbial structure dominated by Proteobacteria, Actinobacteria and Bacteroidetes but after addition of PPCPs, a similar pattern was observed in the relative abundance of the phylum Chloroflexi, the class Sphingobacteriia and the genus Brevundimonas. These biopurification systems can be useful to prevent point source contamination due to the disposal of PPCP-contaminated waters.

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Ketonuria Is Associated with Changes to the Abundance of Roseburia in the Gut Microbiota of Overweight and Obese Women at 16 Weeks Gestation: A Cross-Sectional Observational Study

Nutrients ◽

10.3390/nu11081836 ◽

2019 ◽

Vol 11 (8) ◽

pp. 1836 ◽

Cited By ~ 2

Author(s):

Helen Robinson ◽

Helen Barrett ◽

Luisa Gomez-Arango ◽

H. David McIntyre ◽

Leonie Callaway ◽

...

Keyword(s):

Gut Microbiota ◽

Pregnant Women ◽

Clustering Analysis ◽

Alpha Diversity ◽

Microbiota Composition ◽

Obese Women ◽

Cross Sectional ◽

Low Carbohydrate ◽

Rrna Sequencing ◽

Gut Microbiota Composition

The gut microbiome in pregnancy has been associated with various maternal metabolic and hormonal markers involved in glucose metabolism. Maternal ketones are of particular interest due to the rise in popularity of low-carbohydrate diets. We assessed for differences in the composition of the gut microbiota in pregnant women with and without ketonuria at 16 weeks gestation. Fecal samples were obtained from 11 women with fasting ketonuria and 11 matched controls. The samples were analyzed to assess for differences in gut microbiota composition by 16S rRNA sequencing. Supervised hierarchical clustering analysis showed significantly different beta-diversity between women with and without ketonuria, but no difference in the alpha-diversity. Group comparisons and network analysis showed that ketonuria was associated with an increased abundance of the butyrate-producing genus Roseburia. The bacteria that contributed the most to the differences in the composition of the gut microbiota included Roseburia, Methanobrevibacter, Uncl. RF39, and Dialister in women with ketonuria and Eggerthella, Phascolarctobacterium, Butyricimonas, and Uncl. Coriobacteriaceae in women without ketonuria. This study found that the genus Roseburia is more abundant in the gut microbiota of pregnant women with ketonuria. Roseburia is a butyrate producing bacterium and may increase serum ketone levels.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

Journal of Animal Science ◽

10.1093/jas/skz258.594 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 293-294

Author(s):

Camila S Marcolla ◽

Benjamin Willing

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Poultry Production ◽

Microbiota Composition ◽

Microbial Composition ◽

The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

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Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers

International Journal of Sports Medicine ◽

10.1055/a-1079-5450 ◽

2020 ◽

Vol 41 (05) ◽

pp. 292-299 ◽

Cited By ~ 2

Author(s):

Jarrad Timothy Hampton-Marcell ◽

Tifani W. Eshoo ◽

Marc D. Cook ◽

Jack A. Gilbert ◽

Craig A. Horswill ◽

...

Keyword(s):

Body Composition ◽

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Temporal Dynamics ◽

Fecal Microbiota ◽

Future Research ◽

Training Volume ◽

Short Term ◽

Microbial Composition

AbstractExercise can influence gut microbial community structure and diversity; however, the temporal dynamics of this association have rarely been explored. Here we characterized fecal microbiota in response to short term changes in training volume. Fecal samples, body composition, and training logs were collected from Division I NCAA collegiate swimmers during peak training through their in-season taper in 2016 (n=9) and 2017 (n=7), capturing a systematic reduction in training volume near the conclusion of their athletic season. Fecal microbiota were characterized using 16S rRNA V4 amplicon sequencing and multivariate statistical analysis, Spearman rank correlations, and random forest models. Peak training volume, measured as swimming distance, decreased significantly during the study period from 32.6±4.8 km/wk to 11.3±8.1 km/wk (ANOVA, p<0.05); however, body composition showed no significant changes. Coinciding with the decrease in training volume, the microbial community structure showed a significant decrease in overall microbial diversity, a decrease in microbial community structural similarity, and a decrease in the proportion of the bacterial genera Faecalibacterium and Coprococcus. Together these data demonstrate a significant association between short-term changes in training volume and microbial composition and structure in the gut; future research will establish whether these changes are associated with energy balance or nutrient intake.

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Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources

Animals ◽

10.3390/ani11061718 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1718

Author(s):

Kelang Kang ◽

Yan Hu ◽

Shu Wu ◽

Shourong Shi

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Fecal Microbiota ◽

Metagenomic Analysis ◽

Fecal Samples ◽

Microbial Community Function ◽

Community Function ◽

Rectal Swabs ◽

Gut Microbial Community

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

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Fecal Microbiota Diversity in Survivors of Adolescent/Young Adult Hodgkin Lymphoma

Blood ◽

10.1182/blood.v120.21.1533.1533 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1533-1533

Author(s):

Wendy Cozen ◽

Guoqin Yu ◽

Mitchell Gail ◽

Bharat N. Nathwani ◽

Amie E. Hwang ◽

...

Keyword(s):

Young Adult ◽

Gut Microbiota ◽

Hodgkin Lymphoma ◽

Relative Abundance ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Shannon Index ◽

Tree Index ◽

Unique Otus ◽

Whole Tree

Abstract Abstract 1533 Survivors of adolescent/young adult Hodgkin lymphoma (AYAHL) report fewer exposures to infections during childhood compared to controls. They also have persistent genomic and functional aberrations in their lymphocytes that are partially attributable to chemotherapy or radiotherapy. Recent studies have shown that the gut microbiome can affect both the innate and adaptive immune response, and can suppress or exacerbate an inflammatory response. Given the central role of the gut microbiota in immune function, we investigated whether AYAHL survivors, who were members of 13 mono- and dizygotic twin pairs discordant for this disease, have differences in the diversity or phylogenetic configurations of their fecal microbiota compared to their unaffected co-twins. Twin pairs discordant for AYAHL are an ideal study population because they are at least partially matched on genetic and early life factors, both of which influence the composition of the gut microbiome. Pyrosequencing of bacterial 16S rRNA amplicons generated from single fecal samples obtained from each individual yielded 253,182 filtered and de-noised reads translated into species-level operational taxonomic units (OTUs). Standardized across individuals by random sampling, reads were assigned to 2513 OTUs to compare microbiome diversity and relative abundance of taxa. The number of OTU's was compared between twins using a paired student's t-test and a one-way analysis of variance was performed to determine whether such measures differed across twin pairs by comparing the measures between twins to those of randomly paired individuals. AYAHL survivors had less diverse fecal microbial communities compared to their unaffected co-twin controls by all measures of alpha diversity (Table 1). Measures that weighted the relative abundance of the bacteria were not statistically significantly different (Shannon Index, p= 0.270; Chao index, p= 0.066, PD Whole Tree Index, p= 0.051). However, when the unweighted number of unique OTUs was considered, the difference was significant (338 in cases vs. 369 in unaffected co-twin controls, p= 0.015). When the analysis was restricted to OTUs that were present at an abundance of > 0.1% in at least 2 of the 23 samples analyzed, the differences were attenuated, with only the PD Whole Tree index difference in diversity remaining marginally significant (p= 0.045). Only one bacterial taxon was associated with AYAHL, probably due to chance. Phylogenetic measurements indicated that the bacterial component of the microbiota of co-twins were more similar with respect to one another than unrelated individuals, although no differences by zygosity were observed. These results provide evidence that AYAHL survivors have reduced diversity of the gut microbiota, perhaps as a consequence the disease, its treatment, or a particularly hygienic environment. Table 1. Comparisons of alpha diversity measurements between Hodgkin lymphoma cases and co-twin controls. Measurements of Alpha Diversity Mean (Cases) Mean (Unaffected Co-twins) Mean Difference (Unaffected co-twin-case difference) P-value1 Initial analysis No. unique OTUs 338 369 31 0.015 Shannon index 5.6 5.8 0.2 0.27 Chao1 533 574 41 0.066 PD_whole tree 21.2 22.8 1.6 0.051 Conservative analysis No. unique OTUs 183 196 13 0.10 Shannon index 5.2 5.4 0.2 0.40 Chao1 230 237 7 0.47 PD_whole tree 13.7 14.6 0.9 0.045 1 P-value by paired t-tests. Disclosures: No relevant conflicts of interest to declare.

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The influence of rosuvastatin on the gastrointestinal microbiota and host gene expression profiles

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00149.2016 ◽

2017 ◽

Vol 312 (5) ◽

pp. G488-G497 ◽

Cited By ~ 17

Author(s):

J. A. Nolan ◽

P. Skuse ◽

K. Govindarajan ◽

E. Patterson ◽

N. Konstantinidou ◽

...

Keyword(s):

Gene Expression ◽

Community Structure ◽

Bile Acid ◽

Microbial Community ◽

Gut Microbiota ◽

Acid Metabolism ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Bile Acid Metabolism ◽

Gastrointestinal Microbiota

Statins are the most widely prescribed medications worldwide for the treatment of hypercholesterolemia. They inhibit the activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-R), an enzyme involved in cholesterol synthesis in higher organisms and in isoprenoid biosynthesis in some bacteria. We hypothesized that statins may influence the microbial community in the gut through either direct inhibition or indirect mechanisms involving alterations to host responses. We therefore examined the impact of rosuvastatin (RSV) on the community structure of the murine gastrointestinal microbiota. RSV was orally administered to mice and the effects on the gut microbiota, host bile acid profiles, and markers of inflammation were analyzed. RSV significantly influenced the microbial community in both the cecum and feces, causing a significant decrease in α-diversity in the cecum and resulting in a reduction of several physiologically relevant bacterial groups. RSV treatment of mice significantly affected bile acid metabolism and impacted expression of inflammatory markers known to influence microbial community structure (including RegIIIγ and Camp) in the gut. This study suggests that a commonly used statin (RSV) leads to an altered gut microbial composition in normal mice with attendant impacts on local gene expression profiles, a finding that should prompt further studies to investigate the implications of statins for gut microbiota stability and health in humans. NEW & NOTEWORTHY This work demonstrates that rosuvastatin administration in mice affects the gastrointestinal microbiota, influences bile acid metabolism, and alters transcription of genes encoding factors involved in gut homeostasis and immunity in the gastrointestinal tract.

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