scholarly journals Comparative metagenomic analysis of small ruminants' fecal microbiota

2020 ◽  
Author(s):  
Iman Shabana ◽  
N A Bouqellah ◽  
N N Albakri
Keyword(s):  
Small Ruminants ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Metagenomic Analysis ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Fecal Samples ◽  
Sheep And Goats ◽  
The Core ◽  
Genus Level

Abstract Background Ruminant's gastrointestinal tract inhabits complex microbial communities that influence several aspects of their development and health. Due to the limited knowledge of the fecal microbial population of sheep and goats, the current study aimed to determine the core fecal microbiota of sheep and goats at different ages. Metagenomic analysis was performed by Illumina MiSeq targeting the V3-V4 region of the 16S rRNA genes. Fecal samples were collected from sheep and goats aged 6 months and 12 months, obtained from a single farm. The fecal bacterial composition of both species was investigated at the phylum, class, order, family, and genus levels. Observed Species, Chao1, and Shannon indices were calculated to measure the microbial diversity.Results The core phyla of sheep and goats were Firmicutes (>93.01% in sheep, >95.37% in goat), followed by Proteobacteria (>26.83%in sheep, >62.03% in goat). At the genus level, a total of 36 genera were identified. Of these, 10 genera were identified in both sheep and goats including Escherichia (>40.12%), Clostridium (19.38%), Enterococcus (>5.03%), Lysinibacillus (>76.95%) Streptococcus (>2.83%), Anaerocolumna (>1.63%), Anaerotignum (>35.95%), Muricomes (>0.99%), Tissierella (>0.91%) and Bifidobacterium (>0.51%). Alpha diversity indices indicated that the highest level for the complexity of species diversity was detected in sheep fecal samples at 12 months of age.Conclusion Fecal bacterial metagenomic analysis of sheep and goats showed no significant differences in the microbiota composition on the phyla level. There was an increase in microbiota diversity with age at the genus level. Although analyzing the bacterial composition and diversity is important, further studies on their poten­tial functionality are required.

scholarly journals Colonization and Development of the Fecal Microflora of South China Tiger Cubs (Panthera tigris amoyensis) by Sequencing of the 16S rRNA Gene

2021 ◽  
pp. 1-12
Author(s):  
Yanfa Sun ◽  
Jie Yao ◽  
Min Zhang ◽  
Tengteng Chen ◽  
Weihua Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
South China ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Panthera Tigris ◽  
Gut Health ◽  
Fecal Samples ◽  
Fecal Microflora

Postnatal colonization and development of the gut microbiota is linked to health and growth. A comprehensive understanding of the postnatal compositional changes and development of the microbial community is helpful to understand the gut health and improve the survival rate of South China tiger cubs (<i>Panthera tigris amoyensis</i>). Fecal samples from three tiger cubs were collected on the day of birth in 2018 (June 17–21 [G0], July 18 [G1], July 31 [G2], and August 7 [G3]). The 16S rRNA genes of the fecal microflora were sequenced. Results showed that 38 phyla, 58 classes, 134 orders, 272 families, and 636 genera of bacteria from 3,059 operational taxonomic units were identified from 12 fecal samples. The diversity and abundance of species of group G0 were significantly higher (<i>p</i> &#x3c; 0.05 or 0.01) than those of groups G2 and G3. The predominant phylum was Proteobacteria in groups G0 and G1 (38.85% and 48%, respectively) and Firmicutes in groups G2 and G3 (71.42% and 75.29%, respectively). At the phylum level, the abundance of Deinococcus-Thermus was significantly decreased in groups G1, G2, and G3 as compared to group G0 (<i>p</i> &#x3c; 0.05), while that of Firmicutes was significantly increased in groups G2 and G3 (<i>p</i> &#x3c; 0.05). At the genus level, the abundance of <i>Faecalibacterium</i>, <i>Ralstonia</i>, and unidentified <i>Rickettsiales</i> was significantly decreased in groups G1, G2, and G3 as compared with group G0 (<i>p</i> &#x3c; 0.05), while that of <i>Pseudomonas</i> was significantly decreased in groups G2 and G3 (<i>p</i> &#x3c; 0.05). The composition and structure of fecal microbiota of South China tiger cubs changed after birth.

scholarly journals Vaginal Microbiota of Adolescent Girls Prior to the Onset of Menarche Resemble Those of Reproductive-Age Women

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Roxana J. Hickey ◽  
Xia Zhou ◽  
Matthew L. Settles ◽  
Julie Erb ◽  
Kristin Malone ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Adolescent Girls ◽  
Vaginal Microbiota ◽  
Reproductive Age ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gardnerella Vaginalis ◽  
Bacterial Composition ◽  
Prospective Longitudinal Study ◽  
Prospective Longitudinal

ABSTRACTPuberty is an important developmental stage wherein hormonal shifts mediate the physical and physiological changes that lead to menarche, but until now, the bacterial composition of vaginal microbiota during this period has been poorly characterized. We performed a prospective longitudinal study of perimenarcheal girls to gain insight into the timing and sequence of changes that occur in the vaginal and vulvar microbiota during puberty. The study enrolled 31 healthy, premenarcheal girls between the ages of 10 and 12 years and collected vaginal and vulvar swabs quarterly for up to 3 years. Bacterial composition was characterized by Roche 454 pyrosequencing and classification of regions V1 to V3 of 16S rRNA genes. Contrary to expectations, lactic acid bacteria, primarily Lactobacillus spp., were dominant in the microbiota of most girls well before the onset of menarche in the early to middle stages of puberty.Gardnerella vaginaliswas detected at appreciable levels in approximately one-third of subjects, a notable finding considering that this organism is commonly associated with bacterial vaginosis in adults. Vulvar microbiota closely resembled vaginal microbiota but often exhibited additional taxa typically associated with skin microbiota. Our findings suggest that the vaginal microbiota of girls begin to resemble those of adults well before the onset of menarche.IMPORTANCEThis study addresses longitudinal changes in vaginal and vulvar microbial communities prior to and immediately following menarche. The research is significant because microbial ecology of the vagina is an integral aspect of health, including resistance to infections. The physiologic changes of puberty and initiation of cyclic menstruation are likely to have profound effects on vaginal microbiota, but almost nothing is known about changes that normally occur during this time. Our understanding has been especially hampered by the lack of thorough characterization of microbial communities using techniques that do not rely on the cultivation of fastidious bacteria, as well as a dearth of studies on girls in the early to middle stages of puberty. This study improves our understanding of the normal development of vaginal microbiota during puberty and onset of menarche and may better inform clinical approaches to vulvovaginal care of adolescent girls.

scholarly journals Modulation of the Gut Microbiota by Shen-Yan-Fang-Shuai Formula Improves Obesity Induced by High-Fat Diets

2020 ◽  
Vol 11 ◽  
Author(s):  
Zhen Wang ◽  
Junfeng Lu ◽  
Jingwei Zhou ◽  
Weiwei Sun ◽  
Yang Qiu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Metabolic Disorders ◽  
Intestinal Barrier ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Therapeutic Effects ◽  
Low Grade ◽  
High Fat ◽  
Gut Barrier Function

Obesity and related metabolic disorders are associated with intestinal microbiota dysbiosis, disrupted intestinal barrier and chronic inflammation. Shen-Yan-Fang-Shuai formula (SYFSF) is a traditional Chinese herbal formula composed of Astragali Radix, Radix Angelicae Sinensis, Rheum Officinale Baill, and four other herbs. In this study, we identified that SYFSF treatment prevented weight gain, low-grade inflammation and insulin resistance in high-fat diet (HFD)-fed mice. SYFSF also substantially improved gut barrier function, reduced metabolic endotoxemia, as well as systemic inflammation. Sequencing of 16S rRNA genes obtained from fecal samples demonstrated that SYFSF attenuated HFD-induced gut dysbiosis, seen an decreased Firmicutes to Bacteroidetes ratios. Microbial richness and diversity were also higher in the SYFSF-treated HFD group. Furthermore, similar therapeutic effects and changes in gut microbiota profile caused by SYFSF could be replicated by fecal microbiota transfer (FMT). Taken together, our study highlights the efficacy of SYFSF in preventing obesity and related metabolic disorders. Its therapeutic effect is associated with the modulation of gut microbiota, as a prebiotic.

scholarly journals Effect of Heat Stress on Bacterial Composition and Metabolism in the Rumen of Lactating Dairy Cows

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 925
Author(s):  
Zhao ◽  
Min ◽  
Zheng ◽  
Wang
Keyword(s):  
Heat Stress ◽  
Dairy Cows ◽  
Milk Production ◽  
Dry Matter ◽  
16S Rrna Genes ◽  
Dry Matter Intake ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Rumen Ph ◽  
Lactating Dairy Cows

Heat stress negatively impacts the health and milk production of dairy cows, and ruminal microbial populations play an important role in dairy cattle’s milk production. Currently there are no available studies that investigate heat stress-associated changes in the rumen microbiome of lactating dairy cattle. Improved understanding of the link between heat stress and the ruminal microbiome may be beneficial in developing strategies for relieving the influence of heat stress on ruminants by manipulating ruminal microbial composition. In this study, we investigated the ruminal bacterial composition and metabolites in heat stressed and non-heat stressed dairy cows. Eighteen lactating dairy cows were divided into two treatment groups, one with heat stress and one without heat stress. Dry matter intake was measured and rumen fluid from all cows in both groups was collected. The bacterial 16S rRNA genes in the ruminal fluid were sequenced, and the rumen pH and the lactate and acetate of the bacterial metabolites were quantified. Heat stress was associated with significantly decreased dry matter intake and milk production. Rumen pH and rumen acetate concentrations were significantly decreased in the heat stressed group, while ruminal lactate concentration increased. The influence of heat stress on the microbial bacterial community structure was minor. However, heat stress was associated with an increase in lactate producing bacteria (e.g., Streptococcus and unclassified Enterobacteriaceae), and with an increase in Ruminobacter, Treponema, and unclassified Bacteroidaceae, all of which utilize soluble carbohydrates as an energy source. The relative abundance of acetate-producing bacterium Acetobacter decreased during heat stress. We concluded that heat stress is associated with changes in ruminal bacterial composition and metabolites, with more lactate and less acetate-producing species in the population, which potentially negatively affects milk production.

scholarly journals Effects of Lactococcus lactis on Composition of Intestinal Microbiota: Role of Nisin

2006 ◽  
Vol 72 (1) ◽  
pp. 239-244 ◽  
Author(s):  
Nete Bernbom ◽  
Tine Rask Licht ◽  
Carl-Henrik Brogren ◽  
Birthe Jelle ◽  
Anette H. Johansen ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Intestinal Microbiota ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Enzyme Linked Immunosorbent Assay ◽  
Gradient Gel Electrophoresis ◽  
Intact Molecule ◽  
Human Flora

ABSTRACT This study examined the ability of (i) pure nisin, (ii) nisin-producing Lactococcus lactis strain CHCC5826, and (iii) the non-nisin-producing L. lactis strain CHCH2862 to affect the composition of the intestinal microbiota of human flora-associated rats. The presence of both the nisin-producing and the non-nisin-producing L. lactis strains significantly increased the number of Bifidobacterium cells in fecal samples during the first 8 days but decreased the number of enterococci/streptococci in duodenum, ileum, cecum, and colon samples as detected by selective cultivation. No significant changes in the rat fecal microbiota were observed after dosage with nisin. Pearson cluster analysis of denaturing gradient gel electrophoresis profiles of the 16S rRNA genes present in the fecal microbial population revealed that the microbiota of animals dosed with either of the two L. lactis strains were different from that of control animals dosed with saline. However, profiles of the microbiota from animals dosed with nisin did not differ from the controls. The concentrations of nisin estimated by competitive enzyme-linked immunosorbent assay (ELISA) were approximately 10-fold higher in the small intestine and 200-fold higher in feces than the corresponding concentrations estimated by a biological assay. This indicates that nisin was degraded or inactivated in the gastrointestinal tract, since fragments of this bacteriocin are detected by ELISA while an intact molecule is needed to retain biological activity.

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

Animals ◽  
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.

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

scholarly journals Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

2012 ◽  
Vol 8 (1) ◽  
pp. 231 ◽  
Author(s):  
Samantha M Steelman ◽  
Bhanu P Chowdhary ◽  
Scot Dowd ◽  
Jan Suchodolski ◽  
Jan E Janečka
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fecal Samples ◽  
High Diversity

scholarly journals Bacterial Composition, Community Structure, and Diversity in Apis nigrocincta Gut

2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Christian Apolinaris Lombogia ◽  
Max Tulung ◽  
Jimmy Posangi ◽  
Trina Ekawati Tallei
Keyword(s):  
Community Structure ◽  
Illumina Miseq ◽  
Gut Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Adult Worker ◽  
Gut Microbial Community ◽  
Apis Nigrocincta

Understanding the honeybee gut bacteria is an essential aspect as honeybees are the primary pollinators of many crops. In this study, the honeybee-associated gut bacteria were investigated by targeting the V3-V4 region of 16S rRNA genes using the Illumina MiSeq. The adult worker was captured in an urban area in a dense settlement. In total, 83,018 reads were obtained, revealing six phyla from 749 bacterial operational taxonomic units (OTUs). The gut was dominated by Proteobacteria (58% of the total reads, including Enterobacteriaceae 28.2%, Erwinia 6.43%, and Klebsiella 4.90%), Firmicutes (29% of the total reads, including Lactococcus garvieae 13.45%, Lactobacillus spp. 8.19%, and Enterococcus spp. 4.47%), and Actinobacteria (8% of the total reads, including Bifidobacterium spp. 7.96%). Many of these bacteria belong to the group of lactic acid bacteria (LAB), which was claimed to be composed of beneficial bacteria involved in maintaining a healthy host. The honeybee was identified as Apis nigrocincta based on an identity BLAST search of its COI region. This study is the first report on the gut microbial community structure and composition of A. nigrocincta from Indonesia.

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