scholarly journals Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency

2021 ◽  
Vol 12 ◽  
Author(s):  
Huijiao Lv ◽  
Yun Huang ◽  
Tao Wang ◽  
Shangkun Zhai ◽  
Zhuocheng Hou ◽  
...  
Keyword(s):  
Microbial Community ◽  
Feed Efficiency ◽  
Pearson Correlation ◽  
Alpha Diversity ◽  
Economic Benefits ◽  
Future Research ◽  
Microbial Composition ◽  
Intestinal Microbes ◽  
High Feed ◽  
Dominant Bacteria

The composition of the gut microbiome plays important roles in digestion, nutrient absorption, and health. Here, we analyzed the microbial composition in the duodenum and ileum of yellow broilers. Chickens were grouped based on feed efficiency (high feed efficiency [HFE] and low feed efficiency [LFE] groups; n = 22 each). Microbial samples from the duodenum and ileum were collected, and 16S rRNA sequencing of the V3–V4 region was performed. The dominant bacteria in the duodenum were from the phyla Firmicutes and Cyanobacteria and the genera Lactobacillus, Faecalibacterium, and Ruminococcus. In the ileum, the phyla Firmicutes and Proteobacteria and the genera Lactobacillus, SMB53 and Enterococcus were predominant. Alpha diversity analysis showed that the microbiota diversity was significantly higher in the duodenum than in the ileum. The structure of the ileal microbiota was similar between groups, and the species richness of the microbiota in the HFE group was significantly higher than that in the LFE group. In the HFE and LFE groups, Firmicutes and Cyanobacteria were negatively correlated, and Lactobacillus had medium to high negative correlations with most other genera. Functional prediction analysis showed that the gluconeogenesis I pathway was the most abundant differential metabolic pathway and was significantly altered in the LFE group. Moreover, although the microbial community structures were similar in the duodenum and ileum, the diversity of the microbial community was significantly higher in the duodenum than in the ileum. Pearson correlation analysis revealed that the phylum Chloroflexi and genera Acinetobacter, Pseudomonas, Bacillus and Neisseria were with coefficients <−0.3 or >0.3. In the ileum, Ruminococcus may be associated with HFE whereas Faecalibacterium may be associated with LFE. These findings may provide valuable foundations for future research on composition and diversity of intestinal microbes and provide insights into the roles of intestinal microbes in improving feed efficiency and the industrial economic benefits of yellow broilers.

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

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.

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

2020 ◽  
Vol 41 (05) ◽  
pp. 292-299 ◽  
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.

scholarly journals Biliary microbiota and bile acids composition in cholelithiasis

2018 ◽  
Author(s):  
Vyacheslav A. Petrov ◽  
María A. Fernández-Peralbo ◽  
Rico Derks ◽  
Elena M. Knyazeva ◽  
Nikolay V. Merzlikin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bile Acids ◽  
Acid Concentration ◽  
Gallstone Disease ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Taurocholic Acid ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Taxonomic Profile

AbstractBackgroundA functional interplay between BAs and microbial composition in gut is a well-documented phenomenon. In bile this phenomenon is far less studied and with this report we describe the interactions between the BAs and microbiota in this complex biological matrix.MethodologyThirty-seven gallstone disease patients of which twenty-one withOpisthorchis felineusinfection were enrolled in the study. The bile samples were obtained during laparoscopic cholecystectomy for gallstone disease operative treatment. Common bile acids composition were measured by LC-MS/MS using a column in reverse phase. For all patients gallbladder microbiota was previously analyzed with 16S rRNA gene sequencing on Illumina MiSeq platform. The associations between bile acids composition and microbiota were analysed.Principal findingsBile acids signature andO. felineusinfection status exerts influence on beta-diversity of bile microbial community. Direct correlations were found between taurocholic acid, taurochenodeoxycholic acid concentrations and alpha-diversity of bile microbiota. Taurocholic acid and taurochenodeoxycholic acid both shows positive associations with the presence of Chitinophagaceae family,MicrobacteriumandLutibacteriumgenera andPrevotella intermedia. Also direct associations were identified for taurocholic acid concentration and the presence of Actinomycetales and Bacteroidales orders,Lautropiagenus,Jeotgalicoccus psychrophilusandHaemophilus parainfluenzaeas well as for taurochenodeoxycholic acid and Acetobacteraceae family and Sphingomonas genus. There were no differences in bile acids concentrations between O.felineusinfected and non-infected patients.Conclusions/SignificanceAssociations between diversity, taxonomic profile of bile microbiota and bile acids levels were evidenced in patients with cholelithiasis. Increase of taurochenodeoxycholic acid and taurocholic acid concentration correlates with bile microbiota alpha-diversity and appearance of opportunistic pathogens. Alteration of bile acids signature could cause shifts in bile microbial community structure.

scholarly journals 817. Exploring Microbial Community Alterations during Hospital Animal-Assisted Intervention Programs

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S450-S451
Author(s):  
Kathryn R Dalton ◽  
Karen C Carroll ◽  
Karen C Carroll ◽  
Elizabeth A Grice ◽  
Meghan F Davis
Keyword(s):  
Microbial Community ◽  
Group Therapy ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Therapy Dogs ◽  
Microbial Composition ◽  
Healthcare Facilities ◽  
Therapy Dog ◽  
Therapy Animals ◽  
Before And After

Abstract Background Animal-assisted interventions, or pet therapy, is increasingly used by healthcare facilities given the numerous benefits in various settings. However, therapy animals may serve as vectors of hospital-associated pathogens. Yet, both pathogenic and protective commensal microbes could be transferred between patients and therapy animals. This pilot study aims to quantify the microbial sharing between patients and therapy dogs, and determine if contact level and a decolonization intervention modifies this sharing. Methods We collected pediatric patient and therapy dog nasal samples before and after each group therapy visit. Contact level was based on interaction time and key behaviors. Therapy dog handlers performed normal practices for two control visits, then switched to a decolonization protocol (chlorhexidine shampoo prior to the visit, and chlorhexidine wipes during the visit) for two intervention visits. Sample DNA was sequenced for the 16S rRNA gene V1-3 region to assess microbiota composition and diversity. Results We collected 105 samples (79 from patients and 26 from dogs) over 13 study visits. There was an increase in within-sample (alpha) diversity levels after the visits in patients and dogs in control visits, and an overall decrease in intervention visits. Patients were more similar in their microbial composition (beta diversity) to other patients and to dogs after visits. Patients with higher dog contact were more similar to other patients in control and intervention visits using the unweighted metric, but only in control visits for the weighted metric. Conclusion These findings indicate that microbes are shared between patients and therapy dogs during animal-assisted interventions, shown by the increase in alpha diversity levels and microbial community shifts. High contact increased interactions in all pathways, resulting in greater microbial sharing. With the dog pathway blocked, the intervention reduced spread of unique dog taxa, but sharing still occurred in high contact patients. This shows that, while there is potential for the dog to be a vector, other potential pathways are important for microbial sharing during group therapy visits. Infection control efforts should reflect all possible pathways of microbial transmission. Disclosures All Authors: No reported disclosures

scholarly journals The role of macrobiota in structuring microbial communities along rocky shores

2014 ◽  
Author(s):  
Catherine A Pfister ◽  
Jack A Gilbert ◽  
Sean M Gibbons
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Rocky Shore ◽  
Alpha Diversity ◽  
Rocky Shores ◽  
Microbial Composition ◽  
Habitat Specificity ◽  
Microbial Habitat ◽  
Inert Surfaces

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

scholarly journals Microbial Community Structure and Its Driving Environmental Factors in Black Carp (Mylopharyngodon piceus) Aquaculture Pond

Water ◽  
2021 ◽  
Vol 13 (21) ◽  
pp. 3089
Author(s):  
Xuemei Li ◽  
Lu Liu ◽  
Yongjiu Zhu ◽  
Tingbing Zhu ◽  
Xingbing Wu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Pathogenic Bacteria ◽  
Pearson Correlation ◽  
Microbial Community Composition ◽  
Group Method ◽  
Strongly Correlated ◽  
Microbial Composition ◽  
Black Carp ◽  
Pair Group ◽  
Significant Difference

This study focused on monitoring the dynamics of bacterial communities and assessment of the influences of physicochemical parameters during a culture cycle in black carp polyculture ponds. Our results showed high variation in microbial diversity and microbial composition in the water column during the culture period. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla, while the abundances of the phyla Cyanobacteria, Firmicutes, and Bacteroidetes changed in different months. Moreover, 13 abundant genera with significant difference were found between different months. Thus, samples in different months were divided into three groups according to principal coordinate analysis (PCoA) and unweighted pair-group method (UPGMA) clustering results. RDA showed that total nitrogen (TN), total phosphorus (TP), phosphate (PO43−-P), nitrate (NO3−-N), temperature (T), dissolved oxygen (DO), and pH significantly shaped the microbial community composition in different months. While Pearson correlation coefficient showed that T, SD, and pH were strongly correlated to the dominant genera. Considering some genera are potential pathogenic bacteria, we could manage the black carp pond by quickly monitoring the water temperature and SD in the future.

scholarly journals The role of macrobiota in structuring microbial communities along rocky shores

2014 ◽  
Author(s):  
Catherine A Pfister ◽  
Jack A Gilbert ◽  
Sean M Gibbons
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Rocky Shore ◽  
Alpha Diversity ◽  
Rocky Shores ◽  
Microbial Composition ◽  
Habitat Specificity ◽  
Microbial Habitat ◽  
Inert Surfaces

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

scholarly journals Skin dysbiosis in the microbiome in atopic dermatitis is site-specific and involves bacteria, fungus and virus

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rie Dybboe Bjerre ◽  
Jacob Bak Holm ◽  
Albert Palleja ◽  
Julie Sølberg ◽  
Lone Skov ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Alpha Diversity ◽  
Future Research ◽  
Skin Microbiome ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Site Specific ◽  
Microbial Dysbiosis ◽  
Cutibacterium Acnes ◽  
The Individual

Abstract Background Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the microbial composition at other body sites have not been studied systematically. Objectives The aim of the study is to characterize the skin microbiome, including bacteria, fungi and virus, at different body sites in relation to AD, lesional state, and S. aureus colonization, and to test whether the nares could be a reservoir for S. aureus strain colonization. Methods Using shotgun metagenomics we characterized microbial compositions from 14 well defined skin sites from 10 patients with AD and 5 healthy controls. Results We found clear differences in microbial composition between AD and controls at multiple skin sites, most pronounced on the flexures and neck. The flexures exhibited lower alpha-diversity and were colonized by S. aureus, accompanied by S. epidermidis in lesions. Malassezia species were absent on the neck in AD. Virus mostly constituted Propionibacterium and Staphylococcusphages, with increased abundance of Propionibacterium phages PHL041 and PHL092 and Staphylococcus epidermidis phages CNPH82 and PH15 in AD. In lesional samples, both the genus Staphylococcus and Staphylococcus phages were more abundant. S. aureus abundance was higher across all skin sites except from the feet. In samples where S. aureus was highly abundant, lower abundances of S. hominis and Cutibacterium acnes were observed. M. osloensis and M. luteus were more abundant in AD. By single nucleotide variant analysis of S. aureus we found strains to be subject specific. On skin sites some S. aureus strains were similar and some dissimilar to the ones in the nares. Conclusions Our data indicate a global and site-specific dysbiosis in AD, involving both bacteria, fungus and virus. When defining targeted treatment clinicians should both consider the individual and skin site and future research into potential crosstalk between microbiota in AD yields high potential.

scholarly journals Variations in Microbial Diversity and Metabolite Profiles of Female Landrace Finishing Pigs With Distinct Feed Efficiency

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhixin Wang ◽  
Yingzhi He ◽  
Chuduan Wang ◽  
Hong Ao ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Feed Efficiency ◽  
Growth Traits ◽  
Finishing Pigs ◽  
Feed Conversion ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Functional Annotations ◽  
Carbohydrate Consumption ◽  
High Feed

To enhance pig production, feed efficiency (FE) should be improved; however, the mechanisms by which gut microbes affect FE in pigs have not been fully elucidated. To investigate the differences between the composition and functionality of the gut microbiota associated with low and high FE, microbial compositions were characterized using 16S rRNA sequencing, functional annotations were performed by shotgun metagenomics, and metabolomic profiles were created by GC-TOF-MS from female Landrace finishing pigs with low and high feed conversion ratios (FCRs). Lactobacillus was enriched in the gut microbiota of individuals with low FCRs (and thus high FE), while Prevotella abundance was significantly higher in individuals with high FCRs (and thus low FE). This may be linked to carbohydrate consumption and incomplete digestion. The activity of pathways involved in the metabolism of cofactors and vitamins was greater in pigs with lower FE. We also identified differences in pyruvate-related metabolism, including phenylalanine and lysine metabolism. This suggests that pyruvate metabolism is closely related to microbial fermentation in the colon, which in turn affects glycolysis. This study deepens our understanding of how gut microbiota are related to pig growth traits, and how regulating microbial composition could aid in improving porcine FE. However, these results need to be validated using a larger pig cohort in the future.

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

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

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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