Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

AbstractUnderstanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.

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Altered Gut Microbiota Associated with Hemorrhage in Chronic Radiation Proctitis

10.21203/rs.3.rs-16229/v1 ◽

2020 ◽

Author(s):

Liangzhe Liu ◽

Bingcheng Chen ◽

Chaoyun Chen ◽

Chen Ding ◽

Nana Xiao ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Radiation Proctitis ◽

Rrna Gene ◽

Chronic Radiation Proctitis ◽

Chronic Radiation ◽

Pelvic Cancer ◽

Metagenomic Study ◽

Rrna Gene Sequencing ◽

And Function

Abstract Background: Pelvic cancer radiotherapy may cause chronic radiation proctitis (CRP) that adversely affects patient’s quality of life. Here, we aimed to characterize the gut microbiota of CRP patients and reveal the association of dysbiosis and hematochezia. A comparative metagenomic study of CRP with and without hematochezia was conducted by 16S rRNA gene sequencing. Results: Different patterns of dysbiosis were observed in CRP patients with and without hematochezia. The abundance of Bacteroides was higher in CRP patients without hematochezia. The Verrucomicrobia phylum was enriched while the compositions of the Enterobacteriales family and the Porphyromonadaceae genus were relatively lower in the microbiota of CRP patients with hematochezia. PICRUSt analysis suggested that the expression of Fe-S protein, Glutathione peroxidase and Glutaredoxin-related protein were increased, indicating an exacerbated inflammation state in hematochezia patients. Conclusions: This study provides new insight to the altered composition and function of gut microbiota in patients with hematochezia, implying the link of CRP symptom and bacterial ecosystem on rectal epithelial layer.

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The Impact of Cholecystectomy on the Gut Microbiota: A Case-Control Study

Journal of Clinical Medicine ◽

10.3390/jcm8010079 ◽

2019 ◽

Vol 8 (1) ◽

pp. 79 ◽

Cited By ~ 9

Author(s):

Won Yoon ◽

Han-Na Kim ◽

Eunkyo Park ◽

Seungho Ryu ◽

Yoosoo Chang ◽

...

Keyword(s):

Gut Microbiota ◽

Enterohepatic Circulation ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Microbial Composition ◽

Comprehensive Health ◽

The Difference ◽

Rrna Gene Sequencing ◽

The Impact

Cholecystectomy alters the bile flow into the intestine and the enterohepatic circulation of the bile acids; this may affect the gut microbiota. We assessed the gut microbiota composition of patients who had undergone cholecystectomy and compared with those who had not. From a cohort of 1463 adult participants who underwent comprehensive health screening examinations, 27 subjects who had undergone cholecystectomy (cholecystectomy group) and 81 age- and sex-matched subjects who had not (control group) were selected. Clinical parameters were collected and compared. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from fecal samples. We evaluated differences in the overall microbial composition and in the abundance of taxa. The two groups were comparable with respect to clinical characteristics and laboratory results. The actual number of taxa observed in a sample (observed features) was significantly lower in the cholecystectomy group than in the control group (p = 0.042). The beta diversity of Jaccard distance index was significantly different between the two groups (p = 0.027). Blautia obeum and Veillonella parvula were more abundant in the cholecystectomy group. The difference in the diversity of the gut microbiota between the cholecystectomy and control groups was subtle. However, B. obeum and V. parvula, which have azoreductase activity, were more abundant in the cholecystectomy group. The impact of such changes in the gut microbiota on health remains to be determined.

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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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Prediction of Postoperative Ileus in Patients With Colorectal Cancer by Preoperative Gut Microbiota

Frontiers in Oncology ◽

10.3389/fonc.2020.526009 ◽

2020 ◽

Vol 10 ◽

Author(s):

Ye Jin ◽

Rui Geng ◽

Yang Liu ◽

Lujia Liu ◽

Xiangren Jin ◽

...

Keyword(s):

Colorectal Cancer ◽

Gut Microbiota ◽

Postoperative Ileus ◽

16S Rrna Gene Sequencing ◽

Perioperative Period ◽

Rrna Gene ◽

Microbial Dysbiosis ◽

Auc Value ◽

The Difference ◽

Rrna Gene Sequencing

BackgroundIleus and postoperative ileus (POI) are common complications of colorectal cancer (CRC). However, little is known about the gut microbiota associated with ileus.MethodDifferences in gut microbiota were evaluated by 16S rRNA gene sequencing. We characterized the gut microbiota in 85 CRC patients (cohort 1) and detected differences, and an independent cohort composed of 38 CRC patients (cohort 2) was used to evaluate the results.ResultsThe gut microbiota of CRC patients with and without ileus exhibited large differences in alpha- and beta-diversities and bacterial taxa. The Firmicutes-to-Bacteroidetes ratio and microbial dysbiosis index (MDI) showed greater dysbiosis among ileus patients than among those without ileus. According to the location of CRC, the difference in gut microbiota between patients with and without ileus was more obvious in those with distal CRC than in those with proximal CRC. Finally, Faecalibacterium was significantly reduced in the postoperative perioperative period in patients with ileus. Thus, we used Faecalibacterium as a biomarker for predicting perioperative or POI: the AUC value was 0.74 for perioperative ileus and 0.67 for POI that appeared at 6 months after hospital discharge. The predictive power was evaluated in Cohort 2, with an AUC value of 0.79.ConclusionThese findings regarding difference of gut microbiota in postoperative CRC patients may provide a theoretical basis for the use of microbiota as biomarkers for the prediction of POI.

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Early Gut Microbiota Colonisation of Premature Infants Fed with Breastmilk or Formula with or without Probiotics: A Cohort Study

Nutrients ◽

10.3390/nu13114068 ◽

2021 ◽

Vol 13 (11) ◽

pp. 4068

Author(s):

Cheng Chi ◽

Yali Fan ◽

Cheng Li ◽

Yu Li ◽

Shan Guo ◽

...

Keyword(s):

Cohort Study ◽

Gut Microbiota ◽

Premature Infants ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Feeding Practice ◽

Rrna Gene ◽

The Difference ◽

Rrna Gene Sequencing ◽

Two Stages

Premature infants have a fragile ecology of the gut microbiota, which is associated with many health problems and may be influenced by formula versus breast feeding. The present study investigated differences in the process of gut microbiota colonisation in preterm infants fed with breastmilk or formula with or without probiotics before 12 weeks. This cohort study recruited 138 premature infants; 31 in the breastmilk (BM) group, 59 in the probiotics formula (PF) group and 48 in the non-probiotics formula (NPF) group, according to the feeding practice they received at birth. Gut bacterial composition was identified with 16S rRNA gene sequencing in faecal samples collected at 1 week, 6 weeks and 12 weeks after birth. The alpha diversity was higher in the PF group compared to the other groups at week 1 and 6 (both p < 0.01) but showed no difference at week 12. The beta diversity of the three groups showed a trend towards similarity at the first two stages (p < 0.001 and p = 0.009, respectively) and finally showed no difference at week 12. Canonical redundancy analysis showed that feeding type could explain the difference in gut microbiota composition at week one and six (both p < 0.01). At genus level, Bifidobacterium was enriched in the PF group, while the Enterococcus and Streptococcus was enriched in the NPF group. In summary, formula with probiotics feeding after birth can affect gut microbiota colonisation and lead to a bacterial community with less potential pathogens.

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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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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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Gut microbiota accelerates cisplatin-induced acute liver injury associated with robust inflammation and oxidative stress in mice

Journal of Translational Medicine ◽

10.1186/s12967-021-02814-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Shenhai Gong ◽

Yinglin Feng ◽

Yunong Zeng ◽

Huanrui Zhang ◽

Meiping Pan ◽

...

Keyword(s):

Oxidative Stress ◽

16S Rrna ◽

Gut Microbiota ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Metabolomic Analysis ◽

Rrna Gene Sequencing ◽

And Oxidative Stress

Abstract Background Gut microbiota has been reported to be disrupted by cisplatin, as well as to modulate chemotherapy toxicity. However, the precise role of intestinal microbiota in the pathogenesis of cisplatin hepatotoxicity remains unknown. Methods We compared the composition and function of gut microbiota between mice treated with and without cisplatin using 16S rRNA gene sequencing and via metabolomic analysis. For understanding the causative relationship between gut dysbiosis and cisplatin hepatotoxicity, antibiotics were administered to deplete gut microbiota and faecal microbiota transplantation (FMT) was performed before cisplatin treatment. Results 16S rRNA gene sequencing and metabolomic analysis showed that cisplatin administration caused gut microbiota dysbiosis in mice. Gut microbiota ablation by antibiotic exposure protected against the hepatotoxicity induced by cisplatin. Interestingly, mice treated with antibiotics dampened the mitogen-activated protein kinase pathway activation and promoted nuclear factor erythroid 2-related factor 2 nuclear translocation, resulting in decreased levels of both inflammation and oxidative stress in the liver. FMT also confirmed the role of microbiota in individual susceptibility to cisplatin-induced hepatotoxicity. Conclusions This study elucidated the mechanism by which gut microbiota mediates cisplatin hepatotoxicity through enhanced inflammatory response and oxidative stress. This knowledge may help develop novel therapeutic approaches that involve targeting the composition and metabolites of microbiota.

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Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

Scientific Reports ◽

10.1038/s41598-021-82726-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Francesco Durazzi ◽

Claudia Sala ◽

Gastone Castellani ◽

Gerardo Manfreda ◽

Daniel Remondini ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Shotgun Sequencing ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Experimental Conditions ◽

Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

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Infant Gut Microbiota Associated with Fine Motor Skills

Nutrients ◽

10.3390/nu13051673 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1673

Author(s):

Inmaculada Acuña ◽

Tomás Cerdó ◽

Alicia Ruiz ◽

Francisco J. Torres-Espínola ◽

Ana López-Moreno ◽

...

Keyword(s):

Gut Microbiota ◽

Infant Development ◽

16S Rrna Gene Sequencing ◽

Fine Motor ◽

Rrna Gene ◽

Neurodevelopmental Outcomes ◽

Gut Colonization ◽

Healthy Infants ◽

Behavioural Characteristics ◽

Rrna Gene Sequencing

BACKGROUND: During early life, dynamic gut colonization and brain development co-occur with potential cross-talk mechanisms affecting behaviour. METHODS: We used 16S rRNA gene sequencing to examine the associations between gut microbiota and neurodevelopmental outcomes assessed by the Bayley Scales of Infant Development III in 71 full-term healthy infants at 18 months of age. We hypothesized that children would differ in gut microbial diversity, enterotypes obtained by Dirichlet multinomial mixture analysis and specific taxa based on their behavioural characteristics. RESULTS: In children dichotomized by behavioural trait performance in above- and below-median groups, weighted Unifrac b-diversity exhibited significant differences in fine motor (FM) activity. Dirichlet multinomial mixture modelling identified two enterotypes strongly associated with FM outcomes. When controlling for maternal pre-gestational BMI and breastfeeding for up to 3 months, the examination of signature taxa in FM groups showed that Turicibacter and Parabacteroides were highly abundant in the below-median FM group, while Collinsella, Coprococcus, Enterococcus, Fusobacterium, Holdemanella, Propionibacterium, Roseburia, Veillonella, an unassigned genus within Veillonellaceae and, interestingly, probiotic Bifidobacterium and Lactobacillus were more abundant in the above-median FM group. CONCLUSIONS: Our results suggest an association between enterotypes and specific genera with FM activity and may represent an opportunity for probiotic interventions relevant to treatment for motor disorders.

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