The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys

The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3–V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age groups. In contrast to the adult donkeys, the gut microbiota diversity and richness of the young donkeys showed significantly less resemblance. The microbial data showed that diversity and richness increased with age, but a highly individual variation of microbial composition was observed at month 1. Principal coordinate analysis (PCoA) revealed a significant difference across five time points in the feces. The abundance of Bacteroides, Lactobacillus, and Odoribacter tended to decrease, while the proportion of Streptococcus was significantly increased with age. For functional prediction, the relative abundance of pathways had a significant difference in the feces across different age groups, for example, Terpenoids and Polyketides and Folding, Sorting, and Degradation (P < 0.05 or P < 0.01). The analysis of beta diversity (PCoA and LEfSe) and microbial functions predicted with PICRUSt (NSTIs) clearly divided the donkeys into foals (≤3 months old) and adults (≥7 months old). Microbial community composition and structure had distinctive features at each age group, in accordance with functional stability of the microbiota. Our findings established a framework for understanding the composition and function of the fecal microbiota to differ between young and adult donkeys.

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Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.596750 ◽

2020 ◽

Vol 10 ◽

Author(s):

Xun Kang ◽

Yanhong Wang ◽

Siping Li ◽

Xiaomei Sun ◽

Xiangyang Lu ◽

...

Keyword(s):

Gut Microbiota ◽

Disease Control ◽

Bacterial Communities ◽

Mosquito Species ◽

Microbial Community Composition ◽

Variable Region ◽

Rrna Gene ◽

Microbial Composition ◽

Quality Filtering ◽

And Function

The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3−V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.

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Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.605825 ◽

2021 ◽

Vol 11 ◽

Author(s):

Shiju Xiao ◽

Guangzhong Zhang ◽

Chunyan Jiang ◽

Xin Liu ◽

Xiaoxu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Target Genes ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Phosphotransferase System ◽

Microbial Composition ◽

Kegg Pathways ◽

Significant Difference ◽

Rrna Gene Sequencing ◽

Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

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Liver-specific knockdown of ANGPTL8 alters the structure of the gut microbiota in mice

Annals of Microbiology ◽

10.1186/s13213-020-01599-0 ◽

2020 ◽

Vol 70 (1) ◽

Author(s):

Yinlong Cheng ◽

Yining Li ◽

Yonghong Xiong ◽

Yixin Zou ◽

Siyu Chen ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Shannon Index ◽

Microbiota Composition ◽

Functional Prediction ◽

Adeno Associated Virus ◽

Virus Serotype ◽

Significant Difference ◽

And Function ◽

Gut Microbiota Composition

Abstract Purpose To investigate the effect of liver-specific knockdown of ANGPTL8 on the structure of the gut microbiota. Methods We constructed mice with liver-specific ANGPTL8 knockdown by using an adeno-associated virus serotype 8 (AAV8) system harbouring an ANGPTL8 shRNA. We analysed the structure and function of the gut microbiome through pyrosequencing and KEGG (Kyoto Encyclopedia of Genes and Genomes) functional prediction. Results Compared with controls, ANGPTL8 shRNA reduced the Simpson index and Shannon index (p < 0.01) of the gut microbiota in mice. At the phylum level, the sh-ANGPTL8 group showed a healthier gut microbiota composition than controls (Bacteroidetes: controls 67.52%, sh-ANGPTL8 80.75%; Firmicutes: controls 10.96%, sh-ANGPTL8 8.58%; Proteobacteria: controls 9.29%, sh-ANGPTL8 0.98%; F/B ratio: controls 0.16, sh-ANGPTL8 0.11). PCoA and UPGMA analysis revealed a significant difference in microbiota composition, while KEGG analysis revealed a significant difference in microbiota function between controls and the sh-ANGPTL8 group. Conclusion Our results revealed that inhibition of ANGPTL8 signalling altered the structure of the gut microbiome, which might further affect the metabolism of mice. We have thus identified ANGPTL8 as a novel hepatogenic hormone potentially involving the liver-gut axis and regulating the structure of the gut microbiota.

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Effect of Selected Stilbenoids on Human Fecal Microbiota

Molecules ◽

10.3390/molecules24040744 ◽

2019 ◽

Vol 24 (4) ◽

pp. 744 ◽

Cited By ~ 6

Author(s):

Jose Jaimes ◽

Veronika Jarosova ◽

Ondrej Vesely ◽

Chahrazed Mekadim ◽

Jakub Mrazek ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Statistical Tests ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbial Composition ◽

Genus Clostridium ◽

The Family ◽

Rrna Gene Sequencing

Dietary phenolics or polyphenols are mostly metabolized by the human gut microbiota. These metabolites appear to confer the beneficial health effects attributed to phenolics. Microbial composition affects the type of metabolites produced. Reciprocally, phenolics modulate microbial composition. Understanding this relationship could be used to positively impact health by phenolic supplementation and thus create favorable colonic conditions. This study explored the effect of six stilbenoids (batatasin III, oxyresveratrol, piceatannol, pinostilbene, resveratrol, thunalbene) on the gut microbiota composition. Stilbenoids were anaerobically fermented with fecal bacteria from four donors, samples were collected at 0 and 24 h, and effects on the microbiota were assessed by 16S rRNA gene sequencing. Statistical tests identified affected microbes at three taxonomic levels. Observed microbial composition modulation by stilbenoids included a decrease in the Firmicutes to Bacteroidetes ratio, a decrease in the relative abundance of strains from the genus Clostridium, and effects on the family Lachnospiraceae. A frequently observed effect was a further decrease of the relative abundance when compared to the control. An opposite effect to the control was observed for Faecalibacterium prausnitzii, whose relative abundance increased. Observed effects were more frequently attributed to resveratrol and piceatannol, followed by thunalbene and batatasin III.

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Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children

PeerJ ◽

10.7717/peerj.4663 ◽

2018 ◽

Vol 6 ◽

pp. e4663 ◽

Cited By ~ 6

Author(s):

Shaaz Fareed ◽

Neha Sarode ◽

Frank J. Stewart ◽

Aneeq Malik ◽

Elham Laghaie ◽

...

Keyword(s):

Clostridium Difficile ◽

Adverse Effects ◽

Gut Microbiome ◽

Pediatric Patients ◽

Fecal Microbiota Transplantation ◽

Diversity Index ◽

Microbial Community Composition ◽

Fecal Microbiota ◽

Rrna Gene ◽

Significant Difference

Background Fecal Microbiota Transplantation (FMT) is an innovative means of treating recurrent Clostridium difficile infection (rCDI), through restoration of gut floral balance. However, there is a lack of data concerning the efficacy of FMT and its impact on the gut microbiome among pediatric patients. This study analyzes clinical outcomes and microbial community composition among 15 pediatric patients treated for rCDI via FMT. Methods This is a prospective, observational, pilot study of 15 children ≤18 years, who presented for rCDI and who met inclusion criteria for FMT at a pediatric hospital and pediatric gastroenterology clinic. Past medical history and demographics were recorded at enrollment and subsequent follow-up. Specimens of the donors’ and the patients’ pre-FMT and post-FMT fecal specimen were collected and used to assess microbiome composition via 16S rRNA gene sequencing. Results FMT successfully prevented rCDI episodes for minimum of 3 months post-FMT in all patients, with no major adverse effects. Three patients reported continued GI bleeding; however, all three also had underlying Inflammatory Bowel Disease (IBD). Our analyses confirm a significant difference between pre-and post-FMT gut microbiome profiles (Shannon diversity index), whereas no significant difference was observed between post-FMT and donor microbiome profiles. At the phyla level, post-FMT profiles showed significantly increased levels of Bacteroidetes and significantly decreased levels of Proteobacteria. Subjects with underlying IBD showed no difference in their pre-and post-FMT profiles. Conclusion The low rate of recurrence or re-infection by C. difficile, coupled with minimal adverse effects post-FMT, suggests that FMT is a viable therapeutic means to treat pediatric rCDI. Post-FMT microbiomes are different from pre-FMT microbiomes, and similar to those of healthy donors, suggesting successful establishment of a healthier microbiome.

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Altered fecal microbiota composition in individuals who abuse methamphetamine

Scientific Reports ◽

10.1038/s41598-021-97548-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yongde Yang ◽

Xuan Yu ◽

Xuebing Liu ◽

Guangya Liu ◽

Kuan Zeng ◽

...

Keyword(s):

Gut Microbiota ◽

Negative Symptoms ◽

Microbial Community Composition ◽

Public Health Problem ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Shannon Index ◽

Control Group ◽

Rrna Gene ◽

New Paradigm

AbstractAs a severe public health problem, methamphetamine (METH) abuse places a heavy burden on families and society. A growing amount of evidence has indicated communication between gut microbiota and the CNS in drug addiction, with associations to neural, endocrine and immune pathways. Thus, we searched for alterations in the gut microbiota and their potential effects in METH users through 16S rRNA gene sequencing. A decreased Shannon index indicated lower bacterial diversity in the METH users than in the age-matched control group. The gut microbial community composition in the METH users was also altered, including reductions in Deltaproteobacteria and Bacteroidaceae abundances and increases in Sphingomonadales, Xanthomonadales, Romboutsia and Lachnospiraceae abundances. Moreover, the Fusobacteria abundance was correlated with the duration of METH use. Enterobacteriaceae, Ruminococcaceae, Bacteroides, and Faecalibacterium had statistically significant correlations with items related to the positive and negative symptoms of schizophrenia and to general psychopathology in the METH users, and all have previously been reported to be altered in individuals with psychotic syndromes, especially depression. Abstraction, one of the items of the cognitive assessment, was positively related to Blautia. These findings revealed alterations in the gut microbiota of METH users, and these alterations may play a role in psychotic syndrome and cognitive impairment. Although the mechanisms behind the links between these disorders and METH abuse are unknown, the relationships may indicate similarities in the pathogenesis of psychosis induced by METH abuse and other causes, providing a new paradigm for addiction and METH use disorder treatment.

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Seasonal Changes in the Distinct Taxonomy and Function of the Gut Microbiota in the Wild Ground Squirrel (Spermophilus dauricus)

Animals ◽

10.3390/ani11092685 ◽

2021 ◽

Vol 11 (9) ◽

pp. 2685

Author(s):

Xiaoying Yang ◽

Yuchen Yao ◽

Xueying Zhang ◽

Jiahui Zhong ◽

Fuli Gao ◽

...

Keyword(s):

Gut Microbiota ◽

Breeding Season ◽

Relative Abundance ◽

Ground Squirrel ◽

Microbial Community Composition ◽

Nucleotide Metabolism ◽

Rrna Gene ◽

Seasonal Breeding ◽

And Function ◽

Breeding Seasons

Seasonal breeding is a normal phenomenon in which animals adapt to natural selection and reproduce only in specific seasons. Large studies have reported that the gut microbiota is closely related to reproduction. The purpose of this study was to explore the distinct taxonomy and function of the gut microbiota in the breeding and non-breeding seasons of the wild ground squirrel (Spermophilus dauricus). The 16S rRNA gene sequencing technology was utilized to sequence the gut microbiota of the wild ground squirrel. PICRUSt analysis was also applied to predict the function of the gut microbiota. The results suggested that the main components of the gut microbiota in all samples were Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between the breeding and non-breeding seasons. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were more abundant in the non-breeding season, while Blautia and Streptococcus were more abundant in the breeding season. The results of a functional prediction suggested that the relative abundance of functional categories that were related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism increased in the breeding season. The relative abundance of energy metabolism, transcription, and signal transduction increased in the non-breeding season. Overall, this study found differences in the taxonomy and function of the gut microbiota of the wild ground squirrel between the breeding and non-breeding seasons, and laid the foundation for further studies on the relationship between the gut microbiota and seasonal breeding.

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Gut Microbiota and Metabolome Alterations Associated with Chinese Monks’ Practice

10.21203/rs.3.rs-1198747/v1 ◽

2022 ◽

Author(s):

Tingting Qiao ◽

Ganghua Lu ◽

Zhongwei Lv ◽

Dan Li ◽

Chengyou Jia ◽

...

Keyword(s):

Gut Microbiota ◽

Intestinal Flora ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbial Composition ◽

Rrna Gene Sequencing ◽

And Function ◽

Mental Events ◽

The Relationship

Abstract BackgroundThe practices of monks mainly include long-term vegetarianism and meditation, which are likely to fundamentally influence the gut microbiota and fecal metabolites. We aim to study the relationship between the practices of Chinese monks and gut microbiotas and metabolites.MethodsTwenty-four monks and forty-eight omnivorous controls (never meditated) were included. The microbiotas of all samples were profiled by 16S rRNA gene sequencing, and the metabolomes were examined by nontargeted LC–MS metabolomics. Twenty-four monks were divided into the H group and the L group according to the median time of practice, and microbiota and metabolite analyses were carried out in the two groups.ResultsMicrobial communities and metabolites were decreased in monks. Bacteroidetes was increased in monks, while the Firmicutes, Actinobacteria, and Firmicutes/Bacteroidetes ratios were decreased. At the genus level, Faecalibacterium, Lachnospira, Roseburia, norank_f__Lachnospiraceae, etc. were higher in monks, while Blautia, Eubacterium__hallii_group, Bifidobacteria, etc. were lower (all p < 0.05). Most identical KEGG categories in both Tax4Fun and PICRUSt2 were related to metabolism (6/8, 75.0%). Most higher abundance genera were positively correlated with higher abundance metabolites in monks, indicating that intestinal flora significantly affects intestinal metabolic function. Lipids and lipid-like molecules were the major differential metabolites (VIP >2, p < 0.05) in the two groups. L-dopa plays an important role in many metabolic pathways in monks. Prevotella_9 was enriched in the L group, while norank_f__Lachnospiraceae was enriched in the H group. DG (16:0/18:0/0:0) was highly expressed in the H group and participated in sixteen KEGG functional pathways as well as many immune-related KEGG enrichment pathways.ConclusionThe monks' lifestyle practices of vegetarianism and meditation have the potential to modulate human metabolism and function by affecting the gut microbial composition and metabolites. The appropriate practice of monks makes the intestine younger and increases immunity, but long-term practice may cause adverse physical and mental events.

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Fecal microbial composition and functional diversity of Wuzhishan pigs at different growth stages

AMB Express ◽

10.1186/s13568-021-01249-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mingying Shao ◽

Zhixin Wang ◽

Yingzhi He ◽

Zhen Tan ◽

Jibin Zhang

Keyword(s):

Gut Microbiota ◽

Endocrine System ◽

Fecal Microbiota ◽

Developmental Changes ◽

Growth Stages ◽

Microbial Composition ◽

Other Substances ◽

Almost All ◽

And Function ◽

Different Growth Stages

AbstractThe mammalian gut microbiome participates in almost all life processes in the host. In addition to diet, the breed is the main factor affecting changes in the swine gut microbiota. The composition of the gut microbiota changes significantly during different growth stages. Research on developmental changes in the gut microbiota of indigenous Chinese pig breeds is limited. In this study, the fecal microbiota of Wuzhishan pigs (a Chinese indigenous miniature pig) at different growth stages was investigated using high-throughput 16S rRNA sequencing. Firmicutes and Bacteroidetes were the two dominant phyla, accounting for more than 80% of all sequences. With increasing age, the fecal microbial diversity increased, and the proportion of Firmicutes increased, whereas the proportion of Bacteroidetes decreased. A total of 49 biomarkers with statistical differences were detected in the four growth stages. The different microbiota among groups enhanced the ability to degrade fiber, carbohydrates, and other substances during the growth stages. The endocrine system was different in multiple growth stage paired comparisons, which was attributed to the different body statuses in the growth stages. This study revealed developmental changes in the structure and function of gut microbes in local pigs.

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