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

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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Seasonal Breeding Leads to Changes for Gut Microbiota Diversity in the Wild Ground Squirrel (Spermophilus Dauricus)

10.21203/rs.3.rs-96089/v1 ◽

2020 ◽

Author(s):

Xiaoying Yang ◽

Yuchen Yao ◽

Xueying Zhang ◽

Jiahui Zhong ◽

Fuli Gao ◽

...

Keyword(s):

Gut Microbiota ◽

Community Composition ◽

Breeding Season ◽

Ground Squirrel ◽

Microbial Community Composition ◽

16S Rrna Gene Sequencing ◽

Nucleotide Metabolism ◽

Rrna Gene ◽

Seasonal Breeding ◽

In The Wild

Abstract Background: Seasonal breeding is a normal phenomenon that animals adapt to natural selection and reproduce only in specific seasons. With the gradual popularization of Next-generation sequencing (NGS), large studies have shown that seasonal breeding has been affected by gut microbiota. Consequently, the purpose of this study is to explore the effect of seasonal breeding on the gut microbiota of wild ground squirrel (Spermophilus dauricus). We used 16S rRNA gene sequencing technology to sequence the gut microbiota of the wild ground squirrel in the breeding season and non-breeding season. We also predicted the function of gut microbiota by bioinformatic software.Results: The results showed that the main components of gut microbiota in all samples consisted of Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between these two groups. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were up-regulated in the non-breeding season, while Blautia and Streptococcus spp. were up-regulated in the breeding season. The result of function prediction suggested that the relative abundance of functional categories related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism was higher in the breeding season. The expression of transcription, energy metabolism, and signal transduction was enriched in the non-breeding season. Conclusions: Overall, the results of this study emphasized the significant effects of seasonal breeding on gut microbiota community composition of the wild ground squirrel and laid a foundation for further study of gut microbiota on seasonal breeding in the future.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2020.596394 ◽

2020 ◽

Vol 11 ◽

Author(s):

Jingya Xing ◽

Guiqin Liu ◽

Xinzhuang Zhang ◽

Dongyi Bai ◽

Jie Yu ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Community Composition ◽

Age Groups ◽

Fecal Microbiota ◽

Microbial Colonization ◽

Rrna Gene ◽

Functional Prediction ◽

Microbial Composition ◽

Significant Difference ◽

And Function

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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Two Isomers of Ginger Root Extracts Modify Composition and Function of Gut Microbiota in Rats Treated with Neuropathic Pain

Current Developments in Nutrition ◽

10.1093/cdn/nzaa045_027 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 394-394

Author(s):

Moamen Elmassry ◽

Rui Wang ◽

Abdul Hamood ◽

Volker Neugebauer ◽

Chwan-Li Shen

Keyword(s):

Neuropathic Pain ◽

Gut Microbiota ◽

Relative Abundance ◽

Pentose Phosphate ◽

Control Group ◽

Rrna Gene ◽

Root Extract ◽

Sprague Dawley ◽

Fecal Samples ◽

And Function

Abstract Objectives Emerging evidence has suggested that gut microbiota plays a key role during the development of chronic pain, such as neuropathic pain (NP). This study was to evaluate the effects of two ginger root extract isomers (gingerols and shogaols) on the composition and function of gut microbiota in animals with NP. Methods Sixteen male Sprague-Dawley rats were randomly assigned into 4 groups: sham group, spinal nerve ligation (SNL) group as the pain control group, SNL + gingerols-enriched ginger (GEG) extract group, and SNL + shogaols-enriched ginger (SEG) extract group. Animals in GEG and SEG groups were fed their respective diets on the day of SNL surgery for 30 days. At day 30, fecal samples were collected for microbiota composition and functional analyses. 16S rRNA gene sequencing was conducted from fecal samples and microbiome data analysis was performed with QIIME2 and PICRUSt2. Data were analyzed using non-parametric Kruskal–Wallis test to compare GEG and SEG with SNL group. Results Based on the results of alpha-diversity analyses, neither GEG nor SEG treatment affected the evenness of microbiome. Gingerols or shogaols supplementation into the diet reduced the richness of the gut microbiome, compared to the SNL group. Relative to the SNL group, GEG group had an increase in the relative abundance of the genus Faecalitalea, while SEG group had an increase in the relative abundance of the genus Aerococcus and species Bacteroides massiliensis. In comparison to SNL group, both GEG and SEG groups showed a decrease in the relative abundance of the family Muribaculaceae and the genus Rikenellaceae RC9 gut group. Functional profiling results revealed that relative to the SNL group, both GEG and SEG supplementation increased the proportion of biosynthetic pathways related to energy metabolism (i.e., pentose phosphate pathway and sugar degradation) and peptidoglycan biosynthesis. Furthermore, GEG and SEG differentially modified amino acid-related metabolic pathways, i.e., tyrosine degradation, tryptophan biosynthesis, arginine, and ornithine biosynthesis. Conclusions GEG and SEG exhibited differential effects on the microbiome composition and function, suggesting a prebiotic potential for dietary ginger root intake in the management of NP. Funding Sources Texas Tech University Health Sciences Center.

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Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

Journal of Personalized Medicine ◽

10.3390/jpm11040294 ◽

2021 ◽

Vol 11 (4) ◽

pp. 294

Author(s):

Irina Grigor’eva ◽

Tatiana Romanova ◽

Natalia Naumova ◽

Tatiana Alikina ◽

Alexey Kuznetsov ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Gallstone Disease ◽

Illumina Miseq ◽

Rrna Gene ◽

Bacterial Phyla ◽

Female Patients ◽

Composition And Structure ◽

Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

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Gut microbiota markers associated with obesity and overweight in Italian adults

Scientific Reports ◽

10.1038/s41598-021-84928-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Vanessa Palmas ◽

Silvia Pisanu ◽

Veronica Madau ◽

Emanuela Casula ◽

Andrea Deledda ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Smoking Status ◽

16S Rrna Gene Sequencing ◽

Normal Weight ◽

Activity Level ◽

Rrna Gene ◽

Illumina Platform ◽

Obesity And Overweight ◽

Rrna Gene Sequencing

AbstractIn the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.

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Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽

10.1186/s12885-021-08296-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lito E. Papanicolas ◽

Sarah K. Sims ◽

Steven L. Taylor ◽

Sophie J. Miller ◽

Christos S. Karapetis ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Haematological Malignancy ◽

Amplicon Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Conventional Chemotherapy ◽

Myelosuppressive Chemotherapy ◽

Gram Positive Bacteria ◽

Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

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Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

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Early-Life Stress Modulates Gut Microbiota and Peripheral and Central Inflammation in a Sex-Dependent Manner

International Journal of Molecular Sciences ◽

10.3390/ijms22041899 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1899 ◽

Cited By ~ 1

Author(s):

Hae Jeong Park ◽

Sang A. Kim ◽

Won Sub Kang ◽

Jong Woo Kim

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Life Stress ◽

Early Life ◽

Maternal Separation ◽

Early Life Stress ◽

Female Rats ◽

Rrna Gene ◽

Dependent Manner ◽

Male And Female Rats

Recent studies have reported that changes in gut microbiota composition could induce neuropsychiatric problems. In this study, we investigated alterations in gut microbiota induced by early-life stress (ELS) in rats subjected to maternal separation (MS; 6 h a day, postnatal days (PNDs) 1–21), along with changes in inflammatory cytokines and tryptophan-kynurenine (TRP-KYN) metabolism, and assessed the differences between sexes. High-throughput sequencing of the bacterial 16S rRNA gene showed that the relative abundance of the Bacteroides genus was increased and that of the Lachnospiraceae family was decreased in the feces of MS rats of both sexes (PND 56). By comparison, MS increased the relative abundance of the Streptococcus genus and decreased that of the Staphylococcus genus only in males, whereas the abundance of the Sporobacter genus was enhanced and that of the Mucispirillum genus was reduced by MS only in females. In addition, the levels of proinflammatory cytokines were increased in the colons (IFN-γ and IL-6) and sera (IL-1β) of the male MS rats, together with the elevation of the KYN/TRP ratio in the sera, but not in females. In the hippocampus, MS elevated the level of IL-1β and the KYN/TRP ratio in both male and female rats. These results indicate that MS induces peripheral and central inflammation and TRP-KYN metabolism in a sex-dependent manner, together with sex-specific changes in gut microbes.

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Decreased Enteric Bacterial Composition and Diversity in South American Crohn’s Disease Vary With the Choice of Treatment Strategy and Time Since Diagnosis

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz189 ◽

2019 ◽

Vol 14 (6) ◽

pp. 791-800

Author(s):

Angélica Cruz-Lebrón ◽

Leticia D’argenio Garcia ◽

Aarthi Talla ◽

Samira Joussef-Piña ◽

Miguel E Quiñones-Mateu ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Gut Microbiota ◽

Bacterial Diversity ◽

Relative Abundance ◽

Treatment Strategy ◽

Chronic Inflammatory Disease ◽

Rrna Gene ◽

Faecal Calprotectin ◽

Time Since Diagnosis

Abstract Background and Aims The symptomology of Crohn’s disease [CD], a chronic inflammatory disease of the digestive tract, correlates poorly with clinical, endoscopic or immunological assessments of disease severity. The prevalence of CD in South America is rising, reflecting changes in socio-economic stability. Many treatment options are available to CD patients, including biological agents and corticosteroids, each of which offers variable efficacy attributed to host genetics and environmental factors associated with alterations in the gut microbiota. Methods Based on 16S rRNA gene sequencing and taxonomic differences, we compared the faecal microbial population of Brazilian patients with CD treated with corticosteroid or anti-tumour necrosis factor [anti-TNF] immunotherapy. Faecal calprotectin and plasma sCD14 levels were quantified as markers for local and systemic inflammation, respectively. Results Anti-TNF treatment led to an increased relative abundance of Proteobacteria and a decreased level of Bacteroidetes. In contrast, corticoid treatment was associated with an increase in the relative abundance of Actinobacteria, which has been linked to inflammation in CD. Disruption of the faecal microbiota was related to decreased bacterial diversity and composition. Moreover, the choice of clinical regimen and time since diagnosis modulate the character of the resulting dysbiosis. Conclusions Enteric microbial populations in CD patients who have been treated are modulated by disease pathogenesis, local inflammatory microenvironment and treatment strategy. The dysbiosis that remains after anti-TNF treatment due to decreased bacterial diversity and composition abates restoration of the microbiota to a healthy state, suggesting that the identification and development of new clinical treatments for CD must include their capacity to normalize the gut microbiota.

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