scholarly journals Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5830 ◽  
Author(s):  
Francesco Cicala ◽  
José Alejandro Cisterna-Céliz ◽  
James D. Moore ◽  
Axayácatl Rocha-Olivares
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Structural Changes ◽  
Bacterial Assemblage ◽  
Metabolic Functions ◽  
Abalone Species ◽  
Haliotis Corrugata ◽  
Functional Analyses

The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgensor HF) and yellow (Haliotis corrugataor HC) abalone by16S rRNAgene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed thatMycoplasmadominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone.

scholarly journals Structure, dynamics and predicted functional ecology of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico

2017 ◽  
Author(s):  
Francesco Cicala ◽  
José Alejandro Cisterna-Céliz ◽  
James Douglas Moore ◽  
Axayácatl Rocha-Olivares
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Structural Changes ◽  
Functional Ecology ◽  
Bacterial Assemblage ◽  
Metabolic Functions ◽  
Specific Variation ◽  
Haliotis Corrugata ◽  
Functional Analyses

The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA 454 pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intra-specific variation. This resulted from differences of the species with most reads in each GI metagenome, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found for the explored metabolic pathways between species despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a deep taxonomic and functional split between the microbiota of HF and HC abalone.

scholarly journals Structure, dynamics and predicted functional ecology of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico

2017 ◽  
Author(s):  
Francesco Cicala ◽  
José Alejandro Cisterna-Céliz ◽  
James Douglas Moore ◽  
Axayácatl Rocha-Olivares
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Structural Changes ◽  
Functional Ecology ◽  
Bacterial Assemblage ◽  
Metabolic Functions ◽  
Specific Variation ◽  
Haliotis Corrugata ◽  
Functional Analyses

The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA 454 pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intra-specific variation. This resulted from differences of the species with most reads in each GI metagenome, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found for the explored metabolic pathways between species despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a deep taxonomic and functional split between the microbiota of HF and HC abalone.

scholarly journals A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1070 ◽  
Author(s):  
Puzhi Xu ◽  
Ping Liu ◽  
Changming Zhou ◽  
Yan Shi ◽  
Qingpeng Wu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Infectious Bronchitis Virus ◽  
Metabolic Pathways ◽  
Host Responses ◽  
Integrated Analysis ◽  
Specific Gene ◽  
Rna Seq ◽  
Infectious Bronchitis ◽  
Infection Processes

Chicken gout resulting from nephropathogenic infectious bronchitis virus (NIBV) has become a serious kidney disease problem in chicken worldwide with alterations of the metabolic phenotypes in multiple metabolic pathways. To investigate the mechanisms in chicken responding to NIBV infection, we examined the global transcriptomic and metabolomic profiles of the chicken’s kidney using RNA-seq and GC–TOF/MS, respectively. Furthermore, we analyzed the alterations in cecal microorganism composition in chickens using 16S rRNA-seq. Integrated analysis of these three phenotypic datasets further managed to create correlations between the altered kidney transcriptomes and metabolome, and between kidney metabolome and gut microbiome. We found that 2868 genes and 160 metabolites were deferentially expressed or accumulated in the kidney during NIBV infection processes. These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. In addition, the comprehensive correlations between the kidney metabolome and cecal microbial community showed contributions of gut microbiota in the progression of NIBV-infection. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout.

scholarly journals The Immunologic Role of Gut Microbiota in Patients with Chronic HBV Infection

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Ruilin Yang ◽  
Yao Xu ◽  
Zhifeng Dai ◽  
Xuhong Lin ◽  
Huichao Wang
Keyword(s):  
Hepatitis B ◽  
Gut Microbiota ◽  
Immune Modulation ◽  
Structural Changes ◽  
Hbv Infection ◽  
Chronic Liver Damage ◽  
Chronic Hbv Infection ◽  
Close Relationship ◽  
Chronic Hbv

Hepatitis B can cause acute or chronic liver damage due to hepatitis B virus (HBV) infection. Cirrhosis or hepatocellular carcinoma (HCC) caused by chronic HBV infection often leads to increased mortality. However, the gut and liver have the same embryonic origin; therefore, a close relationship must exist in terms of anatomy and function, and the gut microbiota plays an important role in host metabolic and immune modulation. It is believed that structural changes in the gut microbiota, bacterial translocation, and the resulting immune injury may affect the occurrence and development of liver inflammation caused by chronic HBV infection based on the in-depth cognition of the concept of the “gut-liver axis” and the progress in intestinal microecology. This review aims to summarize and discuss the immunologic role of the gut microbiota in chronic HBV infection.

scholarly journals Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome

2019 ◽  
Vol 20 (2) ◽  
pp. 438 ◽  
Author(s):  
Alejandra Chávez-Carbajal ◽  
Khemlal Nirmalkar ◽  
Ana Pérez-Lizaur ◽  
Fernando Hernández-Quiroz ◽  
Silvia Ramírez-del-Alto ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Lipid Metabolism ◽  
Gut Microbiota ◽  
Metabolic Pathways ◽  
Gut Bacteria ◽  
Mexican Women ◽  
Significant Enrichment ◽  
Prevalence Of Obesity ◽  
High Throughput Dna Sequencing

Obesity is an excessive fat accumulation that could lead to complications like metabolic syndrome. There are reports on gut microbiota and metabolic syndrome in relation to dietary, host genetics, and other environmental factors; however, it is necessary to explore the role of the gut microbiota metabolic pathways in populations like Mexicans, where the prevalence of obesity and metabolic syndrome is high. This study identify alterations of the gut microbiota in a sample of healthy Mexican women (CO), women with obesity (OB), and women with obesity plus metabolic syndrome (OMS). We studied 67 women, characterizing their anthropometric and biochemical parameters along with their gut bacterial diversity by high-throughput DNA sequencing. Our results indicate that in OB or OMS women, Firmicutes was the most abundant bacterial phylum. We observed significant changes in abundances of bacteria belonging to the Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae families and significant enrichment of gut bacteria from 16 different taxa that might explain the observed metabolic alterations between the groups. Finally, the predicted functional metagenome of the gut microbiota found in each category shows differences in metabolic pathways related to lipid metabolism. We demonstrate that Mexican women have a particular bacterial gut microbiota characteristic of each phenotype. There are bacteria that potentially explain the observed metabolic differences between the groups, and gut bacteria in OMS and OB conditions carry more genes of metabolic pathways implicated in lipid metabolism.

scholarly journals Curcumin, Quercetin, Catechins and Metabolic Diseases: The Role of Gut Microbiota

Nutrients ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 206 ◽  
Author(s):  
Umair Shabbir ◽  
Momna Rubab ◽  
Eric Banan-Mwine Daliri ◽  
Ramachandran Chelliah ◽  
Ahsan Javed ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Structural Changes ◽  
Fruits And Vegetables ◽  
Metabolic Diseases ◽  
Structural Diversity ◽  
Gut Health ◽  
Naturally Occurring ◽  
Metabolic Reactions ◽  
Obesity Hypertension

Polyphenols (PPs) are the naturally occurring bioactive components in fruits and vegetables, and they are the most abundant antioxidant in the human diet. Studies are suggesting that ingestion of PPs might be helpful to ameliorate metabolic syndromes that may contribute in the prevention of several chronic disorders like diabetes, obesity, hypertension, and colon cancer. PPs have structural diversity which impacts their bioavailability as they accumulate in the large intestine and are extensively metabolized through gut microbiota (GM). Intestinal microbiota transforms PPs into their metabolites to make them bioactive. Interestingly, not only GM act on PPs to metabolize them but PPs also modulate the composition of GM. Thus, change in GM from pathogenic to beneficial ones may be helpful to ameliorate gut health and associated diseases. However, to overcome the low bioavailability of PPs, various approaches have been developed to improve their solubility and transportation through the gut. In this review, we present evidence supporting the structural changes that occur after metabolic reactions in PPs (curcumin, quercetin, and catechins) and their effect on GM composition that leads to improving overall gut health and helping to ameliorate metabolic disorders.

scholarly journals The Role of Gut Microbiota and Microbiota-Related Serum Metabolites in the Progression of Diabetic Kidney Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Qing Zhang ◽  
Yanmei Zhang ◽  
Lu Zeng ◽  
Guowei Chen ◽  
La Zhang ◽  
...  
Keyword(s):  
Renal Function ◽  
Kidney Disease ◽  
Gut Microbiota ◽  
Metabolic Pathway ◽  
Metabolic Pathways ◽  
Diabetic Kidney Disease ◽  
Intestinal Flora ◽  
Clinical Indicators ◽  
Serum Metabolites

Objective: Diabetic kidney disease (DKD) has become the major cause of end-stage renal disease (ESRD) associated with the progression of renal fibrosis. As gut microbiota dysbiosis is closely related to renal damage and fibrosis, we investigated the role of gut microbiota and microbiota-related serum metabolites in DKD progression in this study.Methods: Fecal and serum samples obtained from predialysis DKD patients from January 2017 to December 2019 were detected using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry, respectively. Forty-one predialysis patients were divided into two groups according to their estimated glomerular filtration rate (eGFR): the DKD non-ESRD group (eGFR ≥ 15 ml/min/1.73 m2) (n = 22), and the DKD ESRD group (eGFR < 15 ml/min/1.73 m2) (n = 19). The metabolic pathways related to differential serum metabolites were obtained by the KEGG pathway analysis. Differences between the two groups relative to gut microbiota profiles and serum metabolites were investigated, and associations between gut microbiota and metabolite concentrations were assessed. Correlations between clinical indicators and both microbiota-related metabolites and gut microbiota were calculated by Spearman rank correlation coefficient and visualized by heatmap.Results: Eleven different intestinal floras and 239 different serum metabolites were identified between the two groups. Of 239 serum metabolites, 192 related to the 11 different intestinal flora were mainly enriched in six metabolic pathways, among which, phenylalanine and tryptophan metabolic pathways were most associated with DKD progression. Four microbiota-related metabolites in the phenylalanine metabolic pathway [hippuric acid (HA), L-(−)-3-phenylactic acid, trans-3-hydroxy-cinnamate, and dihydro-3-coumaric acid] and indole-3 acetic acid (IAA) in the tryptophan metabolic pathway positively correlated with DKD progression, whereas L-tryptophan in the tryptophan metabolic pathway had a negative correlation. Intestinal flora g_Abiotrophia and g_norank_f_Peptococcaceae were positively correlated with the increase in renal function indicators and serum metabolite HA. G_Lachnospiraceae_NC2004_Group was negatively correlated with the increase in renal function indicators and serum metabolites [L-(−)-3-phenyllactic acid and IAA].Conclusions: This study highlights the interaction among gut microbiota, serum metabolites, and clinical indicators in predialysis DKD patients, and provides new insights into the role of gut microbiota and microbiota-related serum metabolites that were enriched in the phenylalanine and tryptophan metabolic pathways, which correlated with the progression of DKD.

scholarly journals Gut Microbiota and Obesity: A Role for Probiotics

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2690 ◽  
Author(s):  
Ludovico Abenavoli ◽  
Emidio Scarpellini ◽  
Carmela Colica ◽  
Luigi Boccuto ◽  
Bahare Salehi ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Current Knowledge ◽  
Obese Patients ◽  
Bacterial Strains ◽  
Literature Searching ◽  
Human Gut ◽  
Unhealthy Lifestyle ◽  
Metabolic Functions ◽  
Gut Microbiota Dysbiosis

Nowadays, obesity is one of the most prevalent human health problems. Research from the last 30 years has clarified the role of the imbalance between energy intake and expenditure, unhealthy lifestyle, and genetic variability in the development of obesity. More recently, the composition and metabolic functions of gut microbiota have been proposed as being able to affect obesity development. Here, we will report the current knowledge on the definition, composition, and functions of intestinal microbiota. We have performed an extensive review of the literature, searching for the following keywords: metabolism, gut microbiota, dysbiosis, obesity. There is evidence for the association between gut bacteria and obesity both in infancy and in adults. There are several genetic, metabolic, and inflammatory pathophysiological mechanisms involved in the interplay between gut microbes and obesity. Microbial changes in the human gut can be considered a factor involved in obesity development in humans. The modulation of the bacterial strains in the digestive tract can help to reshape the metabolic profile in the human obese host as suggested by several data from animal and human studies. Thus, a deep revision of the evidence pertaining to the use probiotics, prebiotics, and antibiotics in obese patients is conceivable

Comparison of the gut microbiota of Rana amurensis and Rana dybowskii under natural winter fasting conditions

2019 ◽  
Vol 366 (21) ◽  
Author(s):  
Qing Tong ◽  
Xiao-peng Du ◽  
Zong-fu Hu ◽  
Li-yong Cui ◽  
Jia Bie ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Operational Taxonomic Unit ◽  
Future Research ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Intestinal Microbes ◽  
Bacterial Phyla ◽  
Significant Enrichment

ABSTRACT Rana amurensis and R. dybowskii occupy similar habitats. As temperatures decrease with the onset of winter, both species migrate to ponds for hibernation. Our goal was to determine whether different species possess different intestinal microbiota under natural winter fasting conditions. We used high-throughput Illumina sequencing of 16S rRNA gene sequences to analyse the diversity of intestinal microbes in the two species. The dominant gut bacterial phyla in both species were Bacteroidetes, Proteobacteria and Firmicutes. Linear discriminant analysis (LDA) effect size revealed significant enrichment of Proteobacteria in R. amurensis and Firmicutes in R. dybowskii. There were significant differences in the gut microbiota composition between the species. The core operational taxonomic unit numbers in R. amurensis and R. dybowskii shared by the two species were 106, 100 and 36. This study indicates that the intestinal bacterial communities of the two frog species are clearly different. Phylum-level analysis showed that R. amurensis was more abundant in Proteobacteria and Verrucomicrobia than R. dybowskii was This is the first study of the composition and diversity of the gut microbiota of these two species, providing important insights for future research on the gut microbiota and the role of these bacterial communities in frogs.

scholarly journals The varying effects of antibiotics on gut microbiota

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lulu Yang ◽  
Ousman Bajinka ◽  
Pa Omar Jarju ◽  
Yurong Tan ◽  
Aji Mary Taal ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Antibiotic Use ◽  
Therapeutic Drugs ◽  
Antibiotic Drug ◽  
Drug Doses ◽  
Animal Feeding ◽  
The Common

AbstractAntibiotics are lifesaving therapeutic drugs that have been used by human for decades. They are used both in the fight against bacterial pathogens for both human and for animal feeding. However, of recent, their effects on the gut microbial compositions and diversities have attracted much attention. Existing literature have established the dysbiosis (reduced diversity) in the gut microbiota in association with antibiotic and antibiotic drug doses. In the light of spelling out the varying effects of antibiotic use on gut microbiota, this review aimed at given an account on the degree of gut microbial alteration caused by common antibiotics. While some common antibiotics are found to destroy the common phyla, other debilitating effects were observed. The effects can be attributed to the mode of mechanism, the class of antibiotic, the degree of resistance of the antibiotic used, the dosage used during the treatment, the route of administration, the pharmacokinetic and pharmacodynamics properties and the spectrum of the antibiotic agent. Health status, stress or the type of diet an individual feeds on could be a great proportion as confounding factors. While it is understood that only the bacterial communities are explored in the quest to establishing the role of gut in health, other gut microbial species are somehow contributing to the dysbiosis status of the gut microbiota. Until now, long term natural fluctuations like diseases outbreaks and mutations of the strain might as well rendered alteration to the gut independent of antibiotic treatments.

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