Multi-omics Study on Gut Microbiota Related to Faecal Microbiota Transplantation

Editorial

22 June 2022

Editorial: Multi-Omics Study on Gut Microbiota Related to Faecal Microbiota Transplantation

Jingtong Wu

Leyi Wang

Yanling Wei

Jialiang Yang

, 7 more and

Zhangran Chen

1,951 views

0 citations

Editors

Zhangran Chen

Shenzhen Wedge Microbiology Research Co.LTD

Yanling Wei

Department of Teaching Support, Army Medical University

Jialiang Yang

Geneis (Beijing) Co. Ltd

Leyi Wang

University of Illinois at Urbana-Champaign

Zeyou Chen

Nankai University

Impact

Original Research

19 April 2022

Ginsenoside Rb1 Improves Metabolic Disorder in High-Fat Diet-Induced Obese Mice Associated With Modulation of Gut Microbiota

Hong Zou

, 20 more and

Guoping Zhao

Gut microbiota plays an important role in metabolic homeostasis. Previous studies demonstrated that ginsenoside Rb1 might improve obesity-induced metabolic disorders through regulating glucose and lipid metabolism in the liver and adipose tissues. Due to low bioavailability and enrichment in the intestinal tract of Rb1, we hypothesized that modulation of the gut microbiota might account for its pharmacological effects as well. Here, we show that oral administration of Rb1 significantly decreased serum LDL-c, TG, insulin, and insulin resistance index (HOMA-IR) in mice with a high-fat diet (HFD). Dynamic profiling of the gut microbiota showed that this metabolic improvement was accompanied by restoring of relative abundance of some key bacterial genera. In addition, the free fatty acids profiles in feces were significantly different between the HFD-fed mice with or without Rb1. The content of eight long-chain fatty acids (LCFAs) was significantly increased in mice with Rb1, which was positively correlated with the increase of Akkermansia and Parasuttereller, and negatively correlated with the decrease of Oscillibacter and Intestinimonas. Among these eight increased LCFAs, eicosapentaenoic acid (EPA), octadecenoic acids, and myristic acid were positively correlated with metabolic improvement. Furthermore, the colonic expression of the free fatty acid receptors 4 (Ffar4) gene was significantly upregulated after Rb1 treatment, in response to a notable increase of LCFA in feces. These findings suggested that Rb1 likely modulated the gut microbiota and intestinal free fatty acids profiles, which should be beneficial for the improvement of metabolic disorders in HFD-fed mice. This study provides a novel mechanism of Rb1 for the treatment of metabolic disorders induced by obesity, which may provide a therapeutic avenue for the development of new nutraceutical-based remedies for treating metabolic diseases, such as hyperlipidemia, insulin resistance, and type 2 diabetes.

5,977 views

24 citations

Relative abundance and functional prediction of bacteria at the genus level. (A) The relative abundance of bacterial DNA at the genus level from the perspective of sample. A0–F0: Two (B and E) of six samples could be positively sequenced for bacterial DNA by the reference protocol; A20I–F20I: Five (A, B, D, E, and F) of six samples could be positively sequenced for bacterial DNA with a one-cycle −20°C freeze-thaw protocol; A20III–F20III: Five (B, C, D, E, and F) of six samples could be positively sequenced for bacterial DNA with a three-cycle −20°C freeze-thaw protocol; A80I–F80I: Three (B, E, and F) of six samples could be positively sequenced for bacterial DNA with a one-cycle −80°C freeze-thaw protocol; A80III–F80III: Two (B and E) of six samples could be positively sequenced for bacterial DNA with a three-cycle −80°C freeze-thaw protocol; ANI–FNI: No samples could be positively sequenced for bacterial DNA with a one-cycle liquid nitrogen freeze-thaw protocol; ANIII–FNIII: Four (A, B, E, and F) of six samples could be positively sequenced for bacterial DNA with a three-cycle liquid nitrogen freeze-thaw protocol; (B) The relative abundance of bacterial DNA at the genus level from the perspective of group; (C) Functional prediction of bacterial DNA among five pretreated groups.

Original Research

09 December 2021

Freeze-Thaw Pretreatment Can Improve Efficiency of Bacterial DNA Extraction From Meconium

Yuntian Xin

, 7 more and

Heqing Shen

5,001 views

13 citations

The expression levels of nine metabolism-associated proteins were highly correlated with the degree of drug-resistance of KPN. (A) Venn diagram summary of the number of up-regulated (up) or down-regulated (down) genes in AMI-resistant (purple), ACB-resistant (pink), and CTX-resistant (blue) isolates, comparing with SEN isolates. The genes only differentially expressed in one of AMI-resistant or CTX-resistant isolates were labeled with dark purple or dark blue, respectively. (B,C) The hist of Pearson correlation coefficients between expression patterns of genes. (D,E) Identification information of metabolic proteins whose expression patterns were significantly correlated with MIC of strains against CTX and AMI.

Original Research

18 November 2021

Comparative Proteomics Demonstrates Altered Metabolism Pathways in Cotrimoxazole- Resistant and Amikacin-Resistant Klebsiella pneumoniae Isolates

Chunmei Shen

, 4 more and

Jingbo Qie

2,607 views

4 citations

Original Research

18 November 2021

Multiomics Study Reveals Enterococcus and Subdoligranulum Are Beneficial to Necrotizing Enterocolitis

Hao Lin

, 6 more and

Jianbo Wen

3,369 views

24 citations

Correction

03 November 2021

Corrigendum: Development and Validation of a Nomogram for the Prediction of Hospital Mortality of Patients With Encephalopathy Caused by Microbial Infection: A Retrospective Cohort Study

Lina Zhao

, 5 more and

Yi Li

1,008 views

1 citations

Original Research

07 October 2021

Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation

Xueying Zhang

, 2 more and

Huanlong Qin

Weighed UniFrac distances of each donor-recipient pair before and after FMT. (A) Each graph shows the changes in distance between recipients and their donor. Fecal microbial profiles of most recipients of Donor 1 and all recipients of Donors 3 and 4 became more similar to those of their donor, while most recipients of Donor 2 showed minimal change or became less similar to those of their donor. (B) PCoA of the microbiota compositions based on UniFrac distances showed the overall beta diversities of the 4 donors and the pre- and post-FMT samples of the 18 patients (left) and of each donor-recipient group (right).

Intestinal dysmotility is common in many diseases and is correlated with gut microbiota dysbiosis and systemic inflammation. Functional constipation (FC) is the most typical manifestation of intestinal hypomotility and reduces patients’ quality of life. Some studies have reported that fecal micriobiota transplantation (FMT) may be an effective and safe therapy for FC as it corrects intestinal dysbiosis. This study was conducted to evaluate how FMT remodels the gut microbiome and to determine a possible correlation between certain microbes and clinical symptoms in constipated individuals. Data were retrospectively collected on 18 patients who underwent FMT between January 1, 2019 and June 30, 2020. The fecal bacterial genome was detected by sequencing the V3–V4 hypervariable regions of the 16S rDNA gene. Fecal short chain fatty acids (SCFAs) were detected by gas chromatography-mass spectrometry, and serum inflammatory factor concentrations were detected via enzyme-linked immunosorbent assay. Comparing the changes in fecal microbiome compositions before and after FMT revealed a significant augmentation in the alpha diversity and increased abundances of some flora such as Clostridiales, Fusicatenibacter, and Paraprevotella. This was consistent with the patients experiencing relief from their clinical symptoms. Abundances of other flora, including Lachnoanaerobaculum, were decreased, which might correlate with the severity of patients’ constipation. Although no differences were found in SCFA production, the butyric acid concentration was correlated with both bacterial alterations and clinical symptoms. Serum IL-8 levels were significantly lower after FMT than at baseline, but IL-4, IL-6, IL-10, and IL-12p70 levels were not noticeably changed. This study showed how FMT regulates the intestinal microenvironment and affects systemic inflammation in constipated patients, providing direction for further research on the mechanisms of FMT. It also revealed potential microbial targets for precise intervention, which may bring new breakthroughs in treating constipation.

6,178 views

42 citations

Correlations of lung imaging features and laboratory findings. Horizontal axis represents biochemical index, and vertical axis represents CT features. Number one indicates p < 0.001, number two indicates p < 0.01, and number three indicates p < 0.05.

Original Research

27 September 2021

Artificial Intelligence Systems for Diagnosis and Clinical Classification of COVID-19

Lan Yu

, 9 more and

Dejun Sun

2,591 views

5 citations

Original Research

16 September 2021

Appendectomy Is Associated With Alteration of Human Gut Bacterial and Fungal Communities

Shuntian Cai

, 7 more and

Hongzhi Xu

Recent research has revealed the importance of the appendix in regulating the intestinal microbiota and mucosal immunity. However, the changes that occur in human gut microbial communities after appendectomy have never been analyzed. We assessed the alterations in gut bacterial and fungal populations associated with a history of appendectomy. In this cross-sectional study, we investigated the association between appendectomy and the gut microbiome using 16S and ITS2 sequencing on fecal samples from 30 healthy individuals with prior appendectomy (HwA) and 30 healthy individuals without appendectomy (HwoA). Analysis showed that the gut bacterial composition of samples from HwA was less diverse than that of samples from HwoA and had a lower abundance of Roseburia, Barnesiella, Butyricicoccus, Odoribacter, and Butyricimonas species, most of which were short-chain fatty acids-producing microbes. The HwA subgroup analysis indicated a trend toward restoration of the HwoA bacterial microbiome over time after appendectomy. HwA had higher gut fungi composition and diversity than HwoA, even 5 years after appendectomy. Compared with those in samples from HwoA, the abundance correlation networks in samples from HwA displayed more complex fungal–fungal and fungal–bacterial community interactions. This study revealed a marked impact of appendectomy on gut bacteria and fungi, which was particularly durable for fungi.

12,400 views

40 citations

Metabolomic profiles of fecal samples from CNV mice and controls. The hierarchical cluster and heat map show the 52 strongly significantly altered metabolites in each sample. Red and blue colors represent high and low levels of metabolites, respectively. The bar graph shows the VIP scores of each metabolite. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.

Original Research

26 August 2021

Altered Fecal Microbiome and Metabolome in a Mouse Model of Choroidal Neovascularization

Yun Li

, 10 more and

Yedi Zhou

5,336 views

15 citations

Original Research

19 August 2021

Development and Validation of a Nomogram for the Prediction of Hospital Mortality of Patients With Encephalopathy Caused by Microbial Infection: A Retrospective Cohort Study

Lina Zhao

, 5 more and

Yi Li

2,829 views

14 citations

The flowchart of prioritization of candidate disease-related microbes.

Original Research

08 July 2021

Prioritizing Disease-Related Microbes Based on the Topological Properties of a Comprehensive Network

Haixiu Yang

, 4 more and

Liang Cheng

2,151 views

2 citations

Schematic diagram of VMT operation. As for donors, first, donors are recruited, preferably from the recipients’ first and second relatives. Second, collect blood/CVF/urine samples of donors and conduct a series of screening by questionnaire, PCR, blood, and urine analysis machines, cultures, microscopy, and NGS. Third, collect CVF sample from qualified healthy donor and process it. It is then transplanted into the recipient’s vagina. As for recipients, first, recipients undergo the same screening process for diagnosis and basic health assessment. Second, recipients are given intravaginal antibiotics to prepare for transplantation. Third, transplant the prepared CVF solution from healthy donor into the recipient’s vagina. Fourth, follow-up studies are carried out on recipients to assess the treatment outcome and adverse effects. VMT, vaginal microbiota transplantation; CVF, cervicovaginal fluid; PCR, polymerase chain reaction; NGS, next-generation sequencing.

Review

18 June 2021

Role of Vaginal Microbiota Dysbiosis in Gynecological Diseases and the Potential Interventions

Yiwen Han

, 1 more and

Tingtao Chen

Vaginal microbiota dysbiosis, characterized by the loss of Lactobacillus dominance and increase of microbial diversity, is closely related to gynecological diseases; thus, intervention on microbiota composition is significant and promising in the treatment of gynecological diseases. Currently, antibiotics and/or probiotics are the mainstay of treatment, which show favorable therapeutic effects but also bring problems such as drug resistance and high recurrence. In this review, we discuss the role of vaginal microbiota dysbiosis in various gynecological infectious and non-infectious diseases, as well as the current and potential interventions.

15,557 views

61 citations

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