scholarly journals Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 730
Author(s):  
E Xu ◽  
Hua Yang ◽  
Minmin Ren ◽  
Yuanxia Wang ◽  
Mingfei Xiao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Short Chain Fatty Acids ◽  
Diversity Indices ◽  
Sensu Stricto ◽  
Shannon Index ◽  
Nutrient Metabolism ◽  
Fecal Samples ◽  
Coa Transferase ◽  
Α Diversity

Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p < 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p < 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p < 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p < 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig’s phenotypic performance and nutrient metabolism.

scholarly journals Developing Gut Microbiota Exerts Colonisation Resistance to Clostridium (syn. Clostridioides) difficile in Piglets

2019 ◽  
Vol 7 (8) ◽  
pp. 218 ◽  
Author(s):  
Grześkowiak ◽  
Dadi ◽  
Zentek ◽  
Vahjen
Keyword(s):  
Gut Microbiota ◽  
Bacterial Community Composition ◽  
Sampling Period ◽  
Diversity Indices ◽  
Sensu Stricto ◽  
Neonatal Piglets ◽  
Clostridioides Difficile ◽  
Fermenting Bacteria ◽  
Suckling Piglets ◽  
Colonisation Resistance

Clostridium (syn. Clostridioides) difficile is considered a pioneer colonizer and may cause gut infection in neonatal piglets. The aim of this study was to explore the microbiota-C. difficile associations in pigs. We used the DNA from the faeces of four sows collected during the periparturient period and from two to three of their piglets (collected weekly until nine weeks of age) for the determination of bacterial community composition (sequencing) and C. difficile concentration (qPCR). Furthermore, C. difficile-negative faeces were enriched in a growth medium, followed by qPCR to verify the presence of this bacterium. Clostridium-sensu-stricto-1 and Lactobacillus spp. predominated the gut microbiota of the sows and their offspring. C. difficile was detected at least once in the faeces of all sows during the entire sampling period, albeit at low concentrations. Suckling piglets harboured C. difficile in high concentrations (up to log10 9.29 copy number/g faeces), which gradually decreased as the piglets aged. Enrichment revealed the presence of C. difficile in previously C. difficile-negative sow and offspring faeces. In suckling piglets, the C. difficile level was negatively correlated with carbohydrate-fermenting bacteria, and it was positively associated with potential pathogens. Shannon and richness diversity indices were negatively associated with the C. difficile counts in suckling piglets. This study showed that gut microbiota seems to set conditions for colonisation resistance against C. difficile in the offspring. However, this conclusion requires further research to include host-specific factors.

scholarly journals Continuous cropping of cut chrysanthemum reduces rhizospheric soil microbial populations, diversity and network complexity

2021 ◽  
Author(s):  
Jun Li ◽  
Xiaoyu Cheng ◽  
Wei Chen ◽  
Hanjie Zhang ◽  
Tianlang Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
Shannon Index ◽  
Continuous Cropping ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Α Diversity ◽  
Soil Bacterial ◽  
The Impact

Abstract Continuous cropping of cut chrysanthemum causes soil degradation and chrysanthemum quality decline, but the biotic and abiotic mechanisms behind it remain unclear. This impedes our ability to assess the true effects of continuous cropping on agricultural soil functions and our ability to repair impaired soils. Here we examined the impact of different replanting years on microbial communities and enzyme activities in rhizosphere soil of cut chrysanthemum (Chrysanthemum morifolium). Our results showed that soil total nitrogen (TN) and organic carbon (SOC) contents were significantly lower in the soil with 12 years of continuous cropping (Y12) than that in the soil with 1 year of cropping (Y1). Compared with Y1, Y12 treatment decreased alkaline phosphatase and β -glucosidase by 12.1 and 24.4%, but increased the activities of soil urease and catalase by 98.2 and 34.8%, respectively. Soil bacterial populations in Y6 (continuous cropping for 6 years) and Y12 treatments decreased by 52.3 and 87.5% compared with that in Y1 treatment. Moreover, the bacterial α-diversity (Shannon index) significantly decreased by 37.3 and 57.6% over 6 and 12 years of continuous cropping, respectively. Long-term monoculture cropping shifted the bacterial community composition, with decreased abundances of dominant phyla such as Proteobacteria and Acidobacteria, but with an increase in the relative abundances of Actinobacteria and Chloroflexi, and Gemmatimonadetes. Moreover, Y6 and Y12 treatments harbored less microbial network complexity, lower bacterial taxa, and fewer linkages among bacterial taxa, relative to Y1. Soil pH, SOC, and TN were the main edaphic factors affecting soil bacterial community compositions and diversity. Overall, our results demonstrate that continuous cropping has a significant negative impact on soil microbial diversity and complexity.

scholarly journals Supplementing Glycerol to Inoculum Induces Changes in pH, SCFA Profiles and Microbiota Composition in In-Vitro Batch Fermentation

Fermentation ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 18
Author(s):  
Qingtao Gao ◽  
Kai Li ◽  
Ruqing Zhong ◽  
Cheng Long ◽  
Lei Liu ◽  
...  
Keyword(s):  
Batch Fermentation ◽  
Fermentation Broth ◽  
Short Chain Fatty Acids ◽  
Shannon Index ◽  
Buffer Solution ◽  
Normal Medium ◽  
Α Diversity ◽  
Propionic Acid Production ◽  
Relative Abundances

Glycerol was generally added to the inoculum as a cryoprotectant. However, it was also a suitable substrate for microbial fermentation, which may produce more SCFAs, thereby decreased pH of the fermentation broth. This study investigated the effect of supplementing glycerol to inoculum on in vitro fermentation and whether an enhanced buffer capacity of medium could maintain the pH stability during in vitro batch fermentation, subsequently improving the accuracy of short chain fatty acids (SCFAs) determination, especially propionate. Two ileal digesta were fermented by pig fecal inoculum with or without glycerol (served as anti-frozen inoculum or frozen inoculum) in standard buffer or enhanced buffer solution (served as normal or modified medium). Along with the fermentation, adding glycerol decreased the pH of fermentation broth (p < 0.05). However, modified medium could alleviate the pH decrement compared with normal medium (p < 0.05). The concentration of total propionic acid production was much higher than that of other SCFAs in anti-frozen inoculum fermentation at 24 and 36 h, thereby increasing the variation (SD) of net production of propionate. The α-diversity analysis showed that adding glycerol decreased Chao1 and Shannon index under normal medium fermentation (p < 0.05) compared to modified medium (p < 0.05) along with fermentation. PCoA showed that all groups were clustered differently (p < 0.01). Adding glycerol improved the relative abundances of Firmicutes, Anaerovibrio, unclassified_f_Selenomonadaceae, and decreased the relative abundance of Proteobacteria (p < 0.05). The relative abundances of Firmicutes, such as Lactobacillus, Blautia and Eubacterium_Ruminantium_group in modified medium with frozen inoculum fermentation were higher than (p < 0.05) those in normal medium at 36 h of incubation. These results showed that adding glycerol in inoculum changed the fermentation patterns, regardless of substrate and medium, and suggested fermentation using frozen inoculum with modified medium could maintain stability of pH, improve the accuracy of SCFA determination, as well as maintain a balanced microbial community.

Vergleichende Analysen des Lungenmikrobioms zwischen Patienten mit ANCA-assoziierten Vaskulitiden und Sarkoidose aus bronchoalveolärer Lavage

2020 ◽  
Vol 2 (4) ◽  
pp. 165-166
Author(s):  
Nicolas Carlos Kahn
Keyword(s):  
High Throughput Sequencing ◽  
Smoking Status ◽  
Bacterial Community Composition ◽  
Negative Relationship ◽  
Human Microbiome ◽  
P Value ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Α Diversity ◽  
The Difference

Microbial involvement in the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, both of which have lung involvement. However, exhaustive research to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed. We sought to elucidate the distinct dysbiotic lung microbiota between AAV and sarcoidosis. We used 16S rRNA gene high-throughput sequencing to obtain the bacterial community composition of bronchoalveolar lavage fluid (BALF) in patients with AAV (n = 16) compared to patients with sarcoidosis (n = 21). The patients had not undergone therapy with immunosuppressive medication when their BALF was acquired. No difference was observed in α-diversity between patients with AAV and patients with sarcoidosis when using all the detected taxa. We defined the taxa of the oral cavity by using the data of oral microbiota of healthy individuals from the Human Microbiome Project (HMP). The analysis using only oral taxa made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. Besides, the analysis using detected taxa except for oral taxa also made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. A linear negative relationship between the α-diversity and Birmingham vasculitis activity score (BVAS) was detected in the AAV group. The observed p-value for the effect of the disease groups on the ß-diversity was small while the effect of other factors including sex and smoking status did not have small p-values. By excluding oral taxa from all the detected taxa, we found a cluster mainly consisted of sarcoidosis patients which was characterized with microbial community monopolized by Erythrobacteraceae family. Our results suggested the importance of considering the influence of oral microbiota in evaluating lung microbiota.

Vergleichende Analysen des Lungenmikrobioms zwischen Patienten mit ANCA-assoziierten Vaskulitiden und Sarkoidose aus bronchoalveolärer Lavage

2020 ◽  
pp. 1-2
Author(s):  
Nicolas Carlos Kahn
Keyword(s):  
High Throughput Sequencing ◽  
Smoking Status ◽  
Bacterial Community Composition ◽  
Negative Relationship ◽  
Human Microbiome ◽  
P Value ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Α Diversity ◽  
The Difference

Microbial involvement in the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, both of which have lung involvement. However, exhaustive research to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed. We sought to elucidate the distinct dysbiotic lung microbiota between AAV and sarcoidosis. We used 16S rRNA gene high-throughput sequencing to obtain the bacterial community composition of bronchoalveolar lavage fluid (BALF) in patients with AAV (n = 16) compared to patients with sarcoidosis (n = 21). The patients had not undergone therapy with immunosuppressive medication when their BALF was acquired. No difference was observed in α-diversity between patients with AAV and patients with sarcoidosis when using all the detected taxa. We defined the taxa of the oral cavity by using the data of oral microbiota of healthy individuals from the Human Microbiome Project (HMP). The analysis using only oral taxa made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. Besides, the analysis using detected taxa except for oral taxa also made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. A linear negative relationship between the α-diversity and Birmingham vasculitis activity score (BVAS) was detected in the AAV group. The observed p-value for the effect of the disease groups on the ß-diversity was small while the effect of other factors including sex and smoking status did not have small p-values. By excluding oral taxa from all the detected taxa, we found a cluster mainly consisted of sarcoidosis patients which was characterized with microbial community monopolized by Erythrobacteraceae family. Our results suggested the importance of considering the influence of oral microbiota in evaluating lung microbiota.

scholarly journals Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2705
Author(s):  
Gercino Ferreira Virgínio Júnior ◽  
Ana Paula da Silva ◽  
Ariany Faria de Toledo ◽  
Milaine Poczynek ◽  
Amanda Moelemberg Cezar ◽  
...  
Keyword(s):  
Basal Diet ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Ruminal Fluid ◽  
Fecal Samples ◽  
Α Diversity ◽  
Holstein Calves ◽  
Hind Gut ◽  
Different Levels

A starter concentrate containing different levels and sources of NDF can modify the gastrointestinal bacteriome. This study evaluated 18 Holstein calves housed in un-bedded suspended individual cages, fed one of three treatments: 22NDF: a conventional starter containing 22% NDF (n = 7); 31NDF: a starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22Hay: diet 22NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily, weaned at 8th week of age, and housed in wood shelters until week 10. To evaluate the bacteriome, the bacterial community of ruminal fluid and fecal samples was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene. Bacterial diversity in rumen was not affected by diet or age. The phyla Firmicutes and Bacteroidota, and Prevotella’ genus were the most abundant in ruminal fluid and fecal samples. In feces, the α-diversity indices were higher for 22Hay. All indices were significantly affected by age. We believe that the ruminal bacteriome was affected by basal diet components, but not affected by NDF levels or sources. The supply of hay was effective in modifying the fecal bacteriome of dairy calves due to hind gut fermentation.

scholarly journals One-Week Effects of Antibiotic Treatment on Gut Microbiota of Late Neonates With Pneumonia or Meningitis

2021 ◽  
Vol 9 ◽  
Author(s):  
Shujing Han ◽  
Qiaoru Zhang ◽  
Yijun Ding ◽  
Ping Chu ◽  
Jinjing Zhang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Antibiotic Treatment ◽  
High Throughput Sequencing ◽  
Healthy Control Group ◽  
Control Group ◽  
Diversity Analysis ◽  
Fecal Samples ◽  
Α Diversity ◽  
Before And After ◽  
Healthy Control

Background: The neonatal period is a critical period for the establishment of the intestinal microbial community. Antibiotics can change the composition of gut microbiota.Methods: Fecal samples were collected from 14 patients with pneumonia and 14 patients with meningitis before and after antibiotic treatment, and fecal samples from five healthy neonates at the 14th and 21st days after birth were collected as well. DNA of fecal samples was extracted, and PCR amplification was performed targeting the V3–V4 variable region of 16S rDNA. After detection by high-throughput sequencing, OTU (operational taxonomic unit) clustering, species annotation, and α diversity analysis were calculated and analyzed statistically.Results: In the healthy control group, the abundance of Bifidobacterium increased significantly from 16.75 to 40.42%, becoming the most dominant bacteria. The results of α diversity analysis suggested that the Sobs indexes of the gut microbiota in the pneumonia and meningitis groups were significantly lower than that in the healthy control group (p &lt; 0.05). PCoA analysis showed that the gut microbiota of pneumonia and meningitis groups clustered distinctly with the control group (Adonis p = 0.001, R2 = 0.565), and there was no significant change in the diversity of gut microbiota before and after the use of antibiotics.Conclusions: The gut microbiota of neonates with infectious diseases were mainly related to the disease conditions. The initial state of neonatal gut microbiome determines its state after 1-week antibiotic treatment. Antibiotic application with 7 days had little effect on the community richness and some effect on the composition of gut microbiota of neonates with pneumonia or meningitis.

scholarly journals Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6684 ◽  
Author(s):  
Siyu Han ◽  
Yu Guan ◽  
Hailong Dou ◽  
Haitao Yang ◽  
Meng Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Invasive Approach ◽  
Fecal Samples ◽  
Significant Difference

The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.

scholarly journals Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease

2019 ◽  
Vol 91 (4) ◽  
pp. 13-20 ◽  
Author(s):  
N A Danilova ◽  
S R Abdulkhakov ◽  
T V Grigoryeva ◽  
M I Markelova ◽  
I Yu Vasilyev ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Gut Microbiota ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Short Chain Fatty Acids ◽  
Reference Database ◽  
Fecal Samples ◽  
Coa Transferase

The results of recent studies indicate a significant role of gut microbiota in the pathogenesis of inflammatory bowel diseases (IBD). The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. Materials and methods. Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. Results and discussion. Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. Conclusion: the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

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