Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea

(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse’s gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.

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The Timing Effects of Soy Protein Intake on Mice Gut Microbiota

Nutrients ◽

10.3390/nu12010087 ◽

2019 ◽

Vol 12 (1) ◽

pp. 87 ◽

Cited By ~ 7

Author(s):

Konomi Tamura ◽

Hiroyuki Sasaki ◽

Kazuto Shiga ◽

Hiroki Miyakawa ◽

Shigenobu Shibata

Keyword(s):

Gut Microbiota ◽

Soy Protein ◽

High Fat Diet ◽

Protein Intake ◽

Short Chain Fatty Acids ◽

16S Rrna Genes ◽

Rrna Genes ◽

Casein Protein ◽

Timing Effects ◽

Microbiota Diversity

Soy protein intake is known to cause microbiota changes. While there are some reports about the effect of soy protein intake on gut microbiota and lipid metabolism, effective timing of soy protein intake has not been investigated. In this study, we examined the effect of soy protein intake timing on microbiota. Mice were fed twice a day, in the morning and evening, to compare the effect of soy protein intake in the morning with that in the evening. Mice were divided into three groups: mice fed only casein protein, mice fed soy protein in the morning, and mice fed soy protein in the evening under high-fat diet conditions. They were kept under the experimental condition for two weeks and were sacrificed afterward. We measured cecal pH and collected cecal contents and feces. Short-chain fatty acids (SCFAs) from cecal contents were measured by gas chromatography. The microbiota was analyzed by sequencing 16S rRNA genes from feces. Soy protein intake whether in the morning or evening led to a greater microbiota diversity and a decrease in cecal pH resulting from SCFA production compared to casein intake. In addition, these effects were relatively stronger by morning soy protein intake. Therefore, soy protein intake in the morning may have relatively stronger effects on microbiota than that in the evening.

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Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study

Microorganisms ◽

10.3390/microorganisms9061237 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1237

Author(s):

Han-Na Kim ◽

Eun-Jeong Joo ◽

Chil-Woo Lee ◽

Kwang-Sung Ahn ◽

Hyung-Lae Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Gastrointestinal Symptoms ◽

Amplicon Sequencing ◽

Recovery Phase ◽

Fecal Samples ◽

Intestinal Microbes ◽

Gut Dysbiosis ◽

16S Rrna Amplicon Sequencing ◽

Microbiome Data ◽

Negative Conversion

Patients with COVID-19 have been reported to experience gastrointestinal symptoms as well as respiratory symptoms, but the effects of COVID-19 on the gut microbiota are poorly understood. We explored gut microbiome profiles associated with the respiratory infection of SARS-CoV-2 during the recovery phase in patients with asymptomatic or mild COVID-19. A longitudinal analysis was performed using the same patients to determine whether the gut microbiota changed after recovery from COVID-19. We applied 16S rRNA amplicon sequencing to analyze two paired fecal samples from 12 patients with asymptomatic or mild COVID-19. Fecal samples were selected at two time points: during SARS-CoV-2 infection (infected state) and after negative conversion of the viral RNA (recovered state). We also compared the microbiome data with those from 36 healthy controls. Microbial evenness of the recovered state was significantly increased compared with the infected state. SARS-CoV-2 infection induced the depletion of Bacteroidetes, while an abundance was observed with a tendency to rapidly reverse in the recovered state. The Firmicutes/Bacteroidetes ratio in the infected state was markedly higher than that in the recovered state. Gut dysbiosis was observed after infection even in patients with asymptomatic or mild COVID-19, while the composition of the gut microbiota was recovered after negative conversion of SARS-CoV-2 RNA. Modifying intestinal microbes in response to COVID-19 might be a useful therapeutic alternative.

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Taxonomic composition and biodiversity of the gut microbiome from patients with irritable bowel syndrome, ulcerative colitis, and asthma

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj21.100 ◽

2022 ◽

Vol 25 (8) ◽

pp. 864-873

Author(s):

A. Y. Tikunov ◽

A. N. Shvalov ◽

V. V. Morozov ◽

I. V. Babkin ◽

G. V. Seledtsova ◽

...

Keyword(s):

Ulcerative Colitis ◽

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Gut Microbiome ◽

Taxonomic Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Taxonomic Structure ◽

Opportunistic Bacteria ◽

Irritable Bowel

To date, the association of an imbalance of the intestinal microbiota with various human diseases, including both diseases of the gastrointestinal tract and disorders of the immune system, has been shown. However, despite the huge amount of accumulated data, many key questions still remain unanswered. Given limited data on the composition of the gut microbiota in patients with ulcerative colitis (UC) and irritable bowel syndrome (IBS) from different parts of Siberia, as well as the lack of data on the gut microbiota of patients with bronchial asthma (BA), the aim of the study was to assess the biodiversity of the gut microbiota of patients with IBS, UC and BA in comparison with those of healthy volunteers (HV). In this study, a comparative assessment of the biodiversity and taxonomic structure of gut microbiome was conducted based on the sequencing of 16S rRNA genes obtained from fecal samples of patients with IBS, UC, BA and volunteers. Sequences of the Firmicutes and Bacteroidetes types dominated in all samples studied. The third most common in all samples were sequences of the Proteobacteria type, which contains pathogenic and opportunistic bacteria. Sequences of the Actinobacteria type were, on average, the fourth most common. The results showed the presence of dysbiosis in the samples from patients compared to the sample from HVs. The ratio of Firmicutes/Bacteroidetes was lower in the IBS and UC samples than in HV and higher the BA samples. In the samples from patients with intestinal diseases (IBS and UC), an increase in the proportion of sequences of the Bacteroidetes type and a decrease in the proportion of sequences of the Clostridia class, as well as the Ruminococcaceae, but not Erysipelotrichaceae family, were found. The IBS, UC, and BA samples had signif icantly more Proteobacteria sequences, including Methylobacterium, Sphingomonas, Parasutterella, Halomonas, Vibrio, as well as Escherichia spp. and Shigella spp. In the gut microbiota of adults with BA, a decrease in the proportion of Roseburia, Lachnospira, Veillonella sequences was detected, but the share of Faecalibacterium and Lactobacillus sequences was the same as in healthy individuals. A signif icant increase in the proportion of Halomonas and Vibrio sequences in the gut microbiota in patients with BA has been described for the f irst time.

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Probiotic Supplementation in a Clostridium difficile-Infected Gastrointestinal Model Is Associated with Restoring Metabolic Function of Microbiota

Microorganisms ◽

10.3390/microorganisms8010060 ◽

2019 ◽

Vol 8 (1) ◽

pp. 60

Author(s):

Mohd Baasir Gaisawat ◽

Chad W. MacPherson ◽

Julien Tremblay ◽

Amanda Piano ◽

Michèle M. Iskandar ◽

...

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

Gastrointestinal Disorder ◽

Short Chain Fatty Acids ◽

Rrna Gene ◽

Metabolic Function ◽

Microbial Composition ◽

Single Strain ◽

Fecal Samples ◽

Metabolic Functions

Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an adjunct is being studied extensively due to their potential to modulate metabolic functions and the gut microbiota. In the present study, we assessed the ability of several single strain probiotics and a probiotic mixture to change the metabolic functions of normal and C. difficile-infected fecal samples. The production of short-chain fatty acids (SCFAs), hydrogen sulfide (H2S), and ammonia was measured, and changes in microbial composition were assessed by 16S rRNA gene amplicon sequencing. The C. difficile-infection in fecal samples resulted in a significant decrease (p < 0.05) in SCFA and H2S production, with a lower microbial alpha diversity. All probiotic treatments were associated with significantly increased (p < 0.05) levels of SCFAs and restored H2S levels. Probiotics showed no effect on microbial composition of either normal or C. difficile-infected fecal samples. These findings indicate that probiotics may be useful to improve the metabolic dysregulation associated with C. difficile infection.

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Modulation of the Gut Microbiota by Shen-Yan-Fang-Shuai Formula Improves Obesity Induced by High-Fat Diets

Frontiers in Microbiology ◽

10.3389/fmicb.2020.564376 ◽

2020 ◽

Vol 11 ◽

Author(s):

Zhen Wang ◽

Junfeng Lu ◽

Jingwei Zhou ◽

Weiwei Sun ◽

Yang Qiu ◽

...

Keyword(s):

Gut Microbiota ◽

Metabolic Disorders ◽

Intestinal Barrier ◽

Fecal Microbiota ◽

16S Rrna Genes ◽

Rrna Genes ◽

Therapeutic Effects ◽

Low Grade ◽

High Fat ◽

Gut Barrier Function

Obesity and related metabolic disorders are associated with intestinal microbiota dysbiosis, disrupted intestinal barrier and chronic inflammation. Shen-Yan-Fang-Shuai formula (SYFSF) is a traditional Chinese herbal formula composed of Astragali Radix, Radix Angelicae Sinensis, Rheum Officinale Baill, and four other herbs. In this study, we identified that SYFSF treatment prevented weight gain, low-grade inflammation and insulin resistance in high-fat diet (HFD)-fed mice. SYFSF also substantially improved gut barrier function, reduced metabolic endotoxemia, as well as systemic inflammation. Sequencing of 16S rRNA genes obtained from fecal samples demonstrated that SYFSF attenuated HFD-induced gut dysbiosis, seen an decreased Firmicutes to Bacteroidetes ratios. Microbial richness and diversity were also higher in the SYFSF-treated HFD group. Furthermore, similar therapeutic effects and changes in gut microbiota profile caused by SYFSF could be replicated by fecal microbiota transfer (FMT). Taken together, our study highlights the efficacy of SYFSF in preventing obesity and related metabolic disorders. Its therapeutic effect is associated with the modulation of gut microbiota, as a prebiotic.

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Effect of pharmacological intakes of zinc and copper on growth performance, circulating cytokines and gut microbiota of newly weaned piglets challenged with coliform lipopolysaccharides

Canadian Journal of Animal Science ◽

10.4141/a05-075 ◽

2006 ◽

Vol 86 (4) ◽

pp. 511-522 ◽

Cited By ~ 35

Author(s):

H. Namkung ◽

J. Gong ◽

H. Yu ◽

C. F. M. de Lange

Keyword(s):

Gut Microbiota ◽

Growth Performance ◽

Plasma Levels ◽

Feed Efficiency ◽

Control Diet ◽

Interactive Effects ◽

16S Rrna Genes ◽

Rrna Genes ◽

Weaned Piglets ◽

Circulating Cytokines

The effect of feeding pharmacological levels of zinc (Zn) and copper (Cu) to newly weaned piglets on growth performance, circulating cytokines levels and gut microbiota was investigated. One hundred eighty piglets [5.90 ± 0.18 kg body weight (BW); six pigs per pen] weaned at 16 to 19 d of age were fed diets containing 3000 ppm additional Zn, 250 ppm additional Cu or a control diet (150 ppm Zn, 15 ppm Cu) for 14 d post-weaning (weeks 1 and 2). Pigs were fed a control diet for an additional 2 wk. Pigs were injected intramuscularly on days 13 and 19 with either 75 μg kg-1 BW of coliform lipopolysaccharide (LPS) or an equivalent amount of saline. Blood samples were collected 3 h after LPS injection to measure plasma levels of cytokines and cortisol. Digesta of ileum and colon were collected from non-challenged pigs on days 14 and 28 to evaluate microbiota using conventional culturing methods and polymerase chain reaction and denaturing gradient gel electrophoresis (PCRDGGE) analysis of the 16S rRNA genes. There were no interactive effects of diet and LPS challenge on growth performance (P > 0.10). Compared with the control, high dietary Zn and Cu increased (P < 0.01) average daily gain (ADG) during weeks 1 (0.125, 0.091 vs. 0.074 kg; P < 0.05) and 2 (0.240, 0.270 vs. 0.155 kg; P < 0.01) only. LPS injection reduced ADG during weeks 2 and 4 (P < 0.01). Dietary treatment did not affect feed efficiency (P > 0.10). Challenging pigs with LPS reduced (P < 0.01) feed efficiency during week 2, but increased (P < 0.05) feed efficiency during week 3. There were no interactive effects between diet and LPS on plasma cytokines levels, except for cortisol (P < 0.05). Plasma levels of cytokines (interleukin-1β, interferon-γ, tumour necrosis factor-α) and cortisol increased (P < 0.01) in pigs challenged with LPS. The high levels of dietary Zn and Cu reduced (P < 0.05) the increases in plasma cortisol level in LPS-challenged pigs at days 9 and 19. There were no differences among the dietary treatments in counts of coliforms and lactobacillus in the digesta from ileum and colon (P > 0.10). PCR-DGGE analysis showed that high levels of dietary Zn and particularly Cu significantly reduced the diversity of ileal microbiota. The effect on microbiota diversity was reversible when dietary Zn and Cu were removed. Enhanced growth performance of the newly weaned piglets fed high dietary Zn and Cu appears mediated via changes in gut microbiota as well as a reduced cortisol response following an immune challenge. Key words: Piglets, zinc, copper, lipopolysaccharide, gut microbiota, cytokines

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Revealing microbial species diversity using sequence capture by hybridization

Microbial Genomics ◽

10.1099/mgen.0.000714 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Sophie Marre ◽

Cyrielle Gasc ◽

Camille Forest ◽

Yacine Lebbaoui ◽

Pascale Mosoni ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rdna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Taxonomic Resolution ◽

Human Gut ◽

Content Type ◽

Innovative Strategy ◽

Human Gut Microbiota ◽

Rare Biosphere

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.

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Although host-related factors are important for the formation of gut microbiota, environmental factors cannot be ignored

10.1101/2020.02.03.933317 ◽

2020 ◽

Author(s):

YeonGyun Jung ◽

Dorsaf Kerfahi ◽

Huy Quang Pham ◽

HyunWoo Son ◽

Jerald Conrad Ibal ◽

...

Keyword(s):

Environmental Factors ◽

Gut Microbiota ◽

Gut Microbiome ◽

Genetic Background ◽

Intestinal Microflora ◽

16S Rrna Genes ◽

Rrna Genes ◽

Related Factors ◽

Present Evidence ◽

The Difference

The gut microbiome is essential to human health. However, little is known about the influence of the environment versus host-related factors (e.g. genetic background, sex, age, and body mass) in the formation of human intestinal microflora. Here, we present evidence in support of the importance of host-related factors in the establishment and maintenance of individual gut assemblages. We collected fecal samples (n = 249) from 44 Korean naval trainees and 39 healthy people living in Korea over eight weeks and sequenced the bacterial 16S rRNA genes. The following hypotheses were tested: 1) microbiome function is linked to its diversity, community structure, and genetic host-related factors, and 2) preexisting host-related factors have a more significant effect on gut microbiome formation and composition than environmental factors. For each individual, the difference between the initial gut microbiota and that after eight weeks was negligible even though the 44 naval trainees lived in the same area and received the same diet, the same amount of exercise, and the same amount of physical stress during the study. This suggests that host-related factors, rather than environmental factors, is a key determinant of individual gut microflora. Moreover, eight weeks of physical training and experiencing the same environmental conditions resulted in an increase in the species Bifidobacterium, Faecalibacterium, and Roseburia in most trainees, suggesting a healthier intestinal environment.

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Analysis of the Salivary Microbiome in the Periodontal Disease patients with hypertension and non-hypertension

Current Bioinformatics ◽

10.2174/1574893615999200728201624 ◽

2020 ◽

Vol 15 ◽

Author(s):

Suhua Li ◽

Rexidan Zaker ◽

Xueqian Chu ◽

Reyida Asihati ◽

Chong Li ◽

...

Keyword(s):

Periodontal Disease ◽

Anaerobic Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

Oral Microbiota ◽

Periodontal Health ◽

Differential Abundance ◽

Operational Taxonomic Units ◽

Hypervariable Regions ◽

Microbiota Diversity

Background: An improved comprehension of the oral microbiota function in the pathogenesis of disease will contribute to diagnosis and treatment for both hypertension and periodontal disease. In our study, a comparison of the salivary microbiome between hypertension and Non-hypertension cohorts was designed to reveal microbial signatures. <P> Methods: Patients were divided into four sub-groups: Gingivitis, Periodontitis (stage 2, 3 and 4). Then the hypertension and Non-hypertension cohorts were split into periodontal health and periodontitis subgroups. The salivary samples were processed for DNA extraction (n=246). The V3-V4 hypervariable regions of microbiome 16S rRNA genes were amplified. Finally, sequencing libraries was constructed and subjected them to bioinformatics and statistical analyses. <P> Results: The oral microbial diversity decreased in both hypertension and periodontal disease groups compared to the healthy. At the genus level, the diversity showed 100 different operational taxonomic units (OTUs) for differential abundance testing. The first trend showed OTUs decreased in relative abundance with increasing periodontal disease, and as well as hypertension groups and non-hypertensive. For this trend OTUs comprised a mix of primarily anaerobic commensals and potential acute diarrhea pathogens. The second trend was that the diversity of genera was decreased in hypertension relative to non-hypertension, including other anaerobic bacteria related with periodontal disease. <P> Conclusions: Microbiota diversity decreased in both hypertension and different stages of periodontal disease groups, however, Neisseria and Solobacterium genera increased in co-existing hypertension and periodontal disease. Obviously, these findings indicate that the abundance of genera continues to change due to additional stresses caused by co-existing conditions

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