Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study

Objectives. Functional prognosis is potentially correlated with gut microbiota alterations following the dysregulation of the gut-microbiota-brain axis after stroke. This study was designed to explore the poststroke alterations of gut microbiota and potential correlations between gut microbiota and global functions. Methods. A total of thirty-eight patients with stroke and thirty-five healthy demographics-matched controls were recruited. Their fecal DNAs were extracted, and the V3-V4 regions of the conserved bacterial 16S RNA were amplified and sequenced on the Illumina MiSeq platform. Microbial composition, diversity indices, and species cooccurrence were compared between groups. Random forest and receiver operating characteristic analysis were used to identify potential diagnostic biomarkers. Relationships between discriminant bacteria and poststroke functional outcomes were estimated. Results. Higher alpha diversity of gut microbiota was observed in poststroke patients as compared to the healthy controls ( p < 0.05 ). Beta diversity showed that microbiota composition in the poststroke group was significantly different from that in the control group. Relative abundance of nine genera increased significantly in poststroke patients, while 82 genera significantly decreased ( p < 0.05 ). The accuracy, specificity, and susceptibility of the optimal model consisted of the top 10 discriminant species were 93%, 100%, and 86%, respectively. Subgroup analysis showed that bacterial taxa abundant between subacute and chronic stroke patients were overall different ( p < 0.05 ). The modified Rankin scale (mRS) ( r = − 0.370 , p < 0.05 ), Fugl-Meyer assessment (FMA) score ( r = 0.364 , p < 0.05 ), water swallow test (WST) ( r = 0.340 , p < 0.05 ), and Barthel index (BI) ( r = 0.349 , p < 0.05 ) were significantly associated with alterations of distinctive gut microbiota. Conclusions. The gut microbiota in patients with stroke was significantly changed in terms of richness and composition. Significant associations were detected between alterations of distinctive gut microbiota and global functional prognosis. It would facilitate novel treatment target selection in the context of stroke while the causal relationships between distinctive gut microbiota alterations and functional variations need to be further verified with well-designed studies.

Download Full-text

Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota

Toxins ◽

10.3390/toxins11010049 ◽

2019 ◽

Vol 11 (1) ◽

pp. 49 ◽

Cited By ~ 6

Author(s):

Winnie-Pui-Pui Liew ◽

Sabran Mohd-Redzwan ◽

Leslie Than

Keyword(s):

Gut Microbiota ◽

Aflatoxin B1 ◽

Lactobacillus Casei ◽

Diversity Index ◽

Alpha Diversity ◽

Diversity Indices ◽

Control Group ◽

Lactobacillus Casei Shirota ◽

Pcr Products ◽

Miseq Platform

Aflatoxin B1 (AFB1) is a ubiquitous carcinogenic food contaminant. Gut microbiota is of vital importance for the host’s health, regrettably, limited studies have reported the effects of xenobiotic toxins towards gut microbiota. Thus, the present study aims to investigate the interactions between AFB1 and the gut microbiota. Besides, an AFB1-binding microorganism, Lactobacillus casei Shirota (Lcs) was tested on its ability to ameliorate the changes on gut microbiota induced by AFB1. The fecal contents of three groups of rats included an untreated control group, an AFB1 group, as well as an Lcs + AFB1 group, were analyzed. Using the MiSeq platform, the PCR products of 16S rDNA gene extracted from the feces were subjected to next-generation sequencing. The alpha diversity index (Shannon) showed that the richness of communities increased significantly in the Lcs + AFB1 group compared to the control and AFB1 groups. Meanwhile, beta diversity indices demonstrated that AFB1 group significantly deviated from the control and Lcs + AFB1 groups. AFB1-exposed rats were especially high in Alloprevotella spp. abundance. Such alteration in the bacterial composition might give an insight on the interactions of AFB1 towards gut microbiota and how Lcs plays its role in detoxification of AFB1.

Download Full-text

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Biology ◽

10.3390/biology10030180 ◽

2021 ◽

Vol 10 (3) ◽

pp. 180

Author(s):

Negash Kabtimer Bereded ◽

Getachew Beneberu Abebe ◽

Solomon Workneh Fanta ◽

Manuel Curto ◽

Herwig Waidbacher ◽

...

Keyword(s):

Gut Microbiota ◽

Nile Tilapia ◽

Alpha Diversity ◽

Environmental Parameters ◽

Illumina Miseq ◽

Microbial Composition ◽

Lake Tana ◽

Future Work ◽

The Impact ◽

Sampling Season

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Download Full-text

Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

Microorganisms ◽

10.3390/microorganisms8071040 ◽

2020 ◽

Vol 8 (7) ◽

pp. 1040

Author(s):

Negash Kabtimer Bereded ◽

Manuel Curto ◽

Konrad J. Domig ◽

Getachew Beneberu Abebe ◽

Solomon Workneh Fanta ◽

...

Keyword(s):

Gut Microbiota ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Large Scale ◽

Alpha Diversity ◽

Illumina Miseq ◽

Operational Taxonomic Units ◽

Nile Tilapia Oreochromis Niloticus ◽

Miseq Platform ◽

Ethiopian Lakes

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

Download Full-text

Metformin Modifies the Gut Microbiota of Mice Infected with Helicobacter pylori

Pharmaceuticals ◽

10.3390/ph14040329 ◽

2021 ◽

Vol 14 (4) ◽

pp. 329

Author(s):

Marine Jauvain ◽

Sarah Courtois ◽

Philippe Lehours ◽

Emilie Bessède

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

Diversity Indices ◽

Digestive Cancer ◽

Pathway Expression ◽

16S Rna ◽

Intestinal Contents ◽

Functional Pathway ◽

H Pylori

Metformin is widely prescribed to treat type 2 diabetes. Diabetes patients treated with metformin have a decreased risk of cancers, including gastric cancer. Among the factors influencing digestive carcinogenesis, gut microbiota interactions have been intensively studied. Metformin exhibits direct antimicrobial activity toward Helicobacterpylori, which plays a crucial role in gastric carcinogenesis. Mice were infected with H. pylori and treated for 12 days with either metformin or phosphate-buffered saline (PBS) as a control. At the end of the treatment period, the mice were euthanized and cecal and intestinal contents and stool were collected. The gut microbiota of the three different digestive sites (stool, cecal, and intestinal contents) were characterized through 16S RNA gene sequencing. In mice infected with H. pylori, metformin significantly decreased alpha diversity indices and led to significant variation in the relative abundance of some bacterial taxa including Clostridium and Lactobacillus, which were directly inhibited by metformin in vitro. PICRUSt analysis suggested that metformin modifies functional pathway expression, including a decrease in nitrate reducing bacteria in the intestine. Metformin significantly changed the composition and predicted function of the gut microbiota of mice infected with H. pylori; these modifications could be implicated in digestive cancer prevention.

Download Full-text

Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath

BMC Veterinary Research ◽

10.1186/s12917-021-03044-z ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Qing Tong ◽

Li-Yong Cui ◽

Jia Bie ◽

Xiao-Yun Han ◽

Zong-Fu Hu ◽

...

Keyword(s):

Gut Microbiota ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Positive Association ◽

Diversity Indices ◽

Control Group ◽

Functional Composition ◽

Significant Positive Association ◽

Collateral Effect

Abstract Background Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined. Results The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high. Conclusions Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota.

Download Full-text

Allium Extract Implements Weaned Piglet’s Productive Parameters by Modulating Distal Gut Microbiota

Antibiotics ◽

10.3390/antibiotics10030269 ◽

2021 ◽

Vol 10 (3) ◽

pp. 269

Author(s):

Miguel Rabelo-Ruiz ◽

Claudia Teso-Pérez ◽

Juan Manuel Peralta-Sánchez ◽

Juan José Ariza ◽

Antonio Manuel Martín-Platero ◽

...

Keyword(s):

Gut Microbiota ◽

Pathogenic Bacteria ◽

Alpha Diversity ◽

Diversity Indices ◽

Daily Weight Gain ◽

Control Group ◽

Growth Promoter ◽

Feed Conversion ◽

Negative Effects ◽

Global Threat

Antimicrobial resistance (AMR) has risen as a global threat for human health. One of the leading factors for this emergence has been the massive use of antibiotics growth-promoter (AGPs) in livestock, enhancing the spread of AMR among human pathogenic bacteria. Thus, several alternatives such as probiotics, prebiotics, or phytobiotics have been proposed for using in animal feeding to maintain or improve productive levels while diminishing the negative effects of AGPs. Reducing the use of antibiotics is a key aspect in the pig rearing for production reasons, as well as for the production of high-quality pork, acceptable to consumers. Here we analyze the potential use of Allium extract as an alternative. In this study, weaned piglets were fed with Allium extract supplementation and compared with control and antibiotic (colistin and zinc oxide) treated piglets. The effects of Allium extract were tested by analyzing the gut microbiome and measuring different productive parameters. Alpha diversity indices decreased significantly in Allium extract group in caecum and colon. Regarding beta diversity, significant differences between treatments appeared only in caecum and colon. Allium extract and antibiotic piglets showed better values of body weight (BW), average daily weight gain (ADG), and feed conversion ratio (FCR) than control group. These results indicate that productive parameters can be implemented by modifying the gut microbiota through phytobiotics such as Allium extract, which will drive to drop the use of antibiotics in piglet diet.

Download Full-text

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe

The Journal of Infectious Diseases ◽

10.1093/infdis/jiz473 ◽

2019 ◽

Cited By ~ 1

Author(s):

Trym T Flygel ◽

Evgeniya Sovershaeva ◽

Shantelle Classen-Weitz ◽

Erik Hjerde ◽

Kilaza S Mwaikono ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Gut Microbiota ◽

Hiv Infection ◽

Alpha Diversity ◽

Illumina Miseq ◽

Hiv Viral Load ◽

Microbial Composition ◽

Cross Sectional ◽

Cd4 Counts ◽

Perinatal Hiv

Abstract Background HIV infection causes impairment of the gastrointestinal barrier, with substantial depletion of CD4+ T-cells in the gut. Antiretroviral therapy (ART) restores CD4+ counts and may have beneficial effects on gut microbiota in adults. Little is known about effect of long-term ART on gut microbiome in HIV infected children. We investigated composition of gut microbiota in HIV infected and uninfected children and assessed associations between gut microbiota and patient characteristics. Methods In a cross-sectional study, rectal swabs were collected from 177 HIV infected and 103 HIV uninfected controls. Gut microbial composition was explored using 16S rRNA sequencing (Illumina Miseq). Results HIV infected children had significantly lower alpha-diversity and higher beta-diversity compared to HIV uninfected. No association was observed between microbiome diversity and CD4+ T-cell count, HIV viral load or HIV-associated chronic lung disease. We found enriched levels of Corynebacterium (p<0.01), Finegoldia (p<0.01) and Anaerococcus (p<0.01) in HIV infected, and enrichment of Enterobacteriaceae (p=0.02) in participants with low CD4+ counts (<400 cells/mm3). Prolonged ART-treatment (≥10 years) was significantly associated with a richer gut microbiota by alpha diversity. Conclusion HIV infected children have altered gut microbiota. Prolonged ART may restore the richness of the microbiota closer to that of HIV-uninfected children.

Download Full-text

Gut microbiota signatures in Schistosoma japonicum infection-induced liver cirrhosis patients: a case–control study

Infectious Diseases of Poverty ◽

10.1186/s40249-021-00821-8 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Qi-Feng Gui ◽

Hui-Lin Jin ◽

Feng Zhu ◽

Hai-Feng Lu ◽

Qin Zhang ◽

...

Keyword(s):

Liver Cirrhosis ◽

Gut Microbiota ◽

Schistosoma Japonicum ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Control Group ◽

Rrna Gene ◽

Healthy Individuals ◽

Rrna Gene Sequencing

Abstract Background Several studies have assessed the role of gut microbiota in various cirrhosis etiologies, however, none has done so in the context of Schistosoma japonicum infection in humans. We, therefore, sought to determine whether gut microbiota is associated with S. japonicum infection-induced liver cirrhosis. Methods From December 2017 to November 2019, 24 patients with S. japonicum infection-induced liver cirrhosis, as well as 25 age- and sex-matched controls from the Zhejiang Province, China, were enrolled. Fecal samples were collected and used for 16S rRNA gene sequencing (particularly, the hypervariable V4 region) using the Illumina MiSeq system. Wilcoxon Rank-Sum and PERMANOVA tests were used for analysis. Results Eight hundred and seven operational taxonomic units (OTUs) were detected, of which, 491 were common between the two groups, whereas 123 and 193 were unique to the control and cirrhosis groups, respectively. Observed species, Chao, ACE, Shannon, Simpson, and Good’s coverage indexes, used for alpha diversity analysis, showed values of 173.4 ± 63.8, 197.7 ± 73.0, 196.3 ± 68.9, 2.96 ± 0.57, 0.13 ± 0.09, and 1.00 ± 0.00, respectively, in the control group and 154.0 ± 68.1, 178.6 ± 75.1, 179.9 ± 72.4, 2.68 ± 0.76, 0.19 ± 0.18, and 1.00 ± 0.00, respectively, in the cirrhosis group, with no significant differences observed between the groups. Beta diversity was evaluated by weighted UniFrac distances, with values of 0.40 ± 0.13 and 0.40 ± 0.11 in the control and cirrhosis groups, respectively (P > 0.05). PCA data also confirmed this similarity (P > 0.05). Meanwhile, the relative abundance of species belonging to the Bacilli class was higher in cirrhosis patients [median: 2.74%, interquartile range (IQR): 0.18–7.81%] than healthy individuals (median: 0.15%, IQR: 0.47–0.73%; P < 0.01), and that of Lactobacillales order was also higher in cirrhosis patients (median: 2.73%, IQR: 0.16–7.80%) than in healthy individuals (median: 0.12%, IQR: 0.03–0.70%; P < 0.05). Conclusions Cumulatively, our results suggest that the gut microbiota of S. japonicum infection-induced liver cirrhosis patients is similar to that of healthy individuals, indicating that bacterial taxa cannot be used as non-invasive biomarkers for S. japonicum infection-induced liver cirrhosis.

Download Full-text

PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

Journal of Animal Science ◽

10.1093/jas/skaa278.729 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 418-419

Author(s):

Gercino F Virgínio Júnior ◽

Milaine Poczynek ◽

Ana Paula Silva ◽

Ariany Toledo ◽

Amanda Cezar ◽

...

Keyword(s):

Illumina Miseq ◽

Diversity Indices ◽

Dairy Calves ◽

Rrna Gene ◽

Gastrointestinal Microbiome ◽

Fecal Microbiome ◽

Miseq Platform ◽

Holstein Calves ◽

Ad Libitum ◽

Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

Download Full-text

The change of gut microbiota in MDD patients under SSRIs treatment

Scientific Reports ◽

10.1038/s41598-021-94481-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yang Shen ◽

Xiao Yang ◽

Gaofei Li ◽

Jiayu Gao ◽

Ying Liang

Keyword(s):

Gut Microbiota ◽

Maximum Dose ◽

Antidepressant Treatment ◽

Intestinal Flora ◽

Alpha Diversity ◽

The Other ◽

Control Group ◽

Depressed Patients ◽

Metabolic Functions

AbstractThe alterations in the gut microbiota have been reported to be correlated with the development of depression. The purpose of this study was to investigate the changes of intestinal microbiota in depressed patients after antidepressant treatment. We recruited 30 MDD patients (MDD group) and 30 healthy controls (control group). The MDD group received individualized treatment with escitalopram at a maximum dose of 20 mg/day. After depressive symptoms improved to a HAMD scale score > 50%, a fecal sample was collected again and used as the follow-up group. The differences of gut microbiota between patients and controls, the characteristics of gut microbiota under treatment and the potential differences in metabolic functions were thus investigated. The Firmicutes/Bacteroidetes ratio was significantly different within three groups, and the ratio of follow-up group was significantly lower than those of the other two groups. Alpha diversity was significantly higher in MDD group than those of the other groups, and the alpha diversity was not significantly different between control and follow-up groups. The beta diversity of some patients resembled participants in the control group. The metabolic function of gut microbiota after treatment was still different from that of the control group. This study suggests that the intestinal flora of depressed patients has a tendency to return to normal under escitalopram treatment.

Download Full-text