Intestinal flora will continue to be hot in 2021

Click【Medical Formula】Focus on us In the past ten years, more and more studies have shown that intestinal flora and inflammatory bowel disease (IBD) are related.

Due to the lack of longitudinal studies of the gut microbiota and pre-diagnosis data, it is not clear whether the changes in the gut microbiome are the cause or the result of inflammatory bowel disease.

Today I will introduce this gut microbiota article published in Gastroenterology in January 2021.

A research team from the Netherlands conducted a study on the intestinal microbiota of IBD twins, collecting stool samples from healthy, IBD twins, healthy people and unrelated IBD patients (matched by age, gender and BMI) for metagenomic sequencing and analysis It was found that healthy twins have the same gut microbial characteristics as IBD twins and unrelated IBD patients.

Among them, there are overlapping species and pathways in the intestines of healthy twins, IBD twins and unrelated IBD patients.

The shared pathways include potential inflammation-related pathways, such as propionic acid degradation and increased L-arginine degradation pathways, indicating that the intestinal microbiota of IBD twins and healthy twins have similar IBD characteristics.
These similar IBD microbiota characteristics may be the first For the occurrence of IBD.

Researchers say that gut microbes play an important role in the pathogenesis of IBD.

1.
Experimental and analytical methods (1) Grouping design: This cross-sectional study included 2 groups of subjects: ①99 IBD twins and healthy twins (from 51 pairs) older than 16 years old, the subjects were in Utrecht University The Medical Center (UMC) conducts longitudinal follow-up (evaluation every 6 months) during which blood, urine, stool, oropharyngeal swabs, and colorectal biopsy samples are collected.

②Healthy controls (495 patients) and unrelated IBD patients (99 patients) whose age, gender and BMI matched those of twin patients.

(2) Sample collection: For the twin cohort, the stool samples are now stored at room temperature after being collected, and then frozen in the -80℃ refrigerator within 31 hours; in the cohort of healthy people and IBD patients, the stool samples are frozen first after collection- 20°C refrigerator (in the subject's home), then transported to the research facility via dry ice and frozen in a -80°C refrigerator.

(3) DNA extraction and sequencing: microorganisms are separated and extracted by QIAamp Fast DNA Stool Mini Kit, and then metagenomic sequencing is performed on the Illumina HiSeq 2000 platform.

(4) Quality control: The original data is removed through KneadData and trimmed (PHRED quality>30), then Bowtie2 is used to remove the sequence aligned to the human reference genome (GRCh37/hg19), and FastQC is used to check the data quality.

MetaPhlAn2 was used to analyze the metagenome classification and composition of the sequence, and HUMAnN2 was used to predict the function of the metagenomic group.

(5) Data analysis process: first compare the intestinal microbiota of healthy twins and IBD twins, and then compare the intestinal microbiota of healthy twins, IBD twins, IBD patients and healthy controls.

Analyze the following aspects: ①α and β diversity; ②Analyze the similarity of intestinal microbiota based on the consistency, phenotype, conjugation and cohabitation of IBD between individuals; ③Assess the relative abundance of microbial species and functions in different cohorts Differences and overlaps.

(6) Statistical analysis: All analysis is done by R language (code: https://github.
com/WeersmaLabIBD/Microbiome/blob/master/IBD_Twins_Microbiome_Utrecht_Groningen.
md) 2.
Results 2.
1 Subjects and sample characteristics recruited a total of 99 twins (51 pairs) and 495 healthy controls matched with age, sex, and BMI, and 99 unrelated IBD patients were enrolled.

Of the 99 twins, 53 are identical twins and 46 are fraternal twins.

Among the 51 pairs of twins, there are 12 pairs of identical IBD, and 39 pairs of disagreements (only one of them has IBD).

Twins and unrelated IBD patients with a history of appendectomy and antibiotic or PPI use are more common than healthy controls.

More IBD twins were diagnosed with CD (54.
1% vs 28.
3%).

2.
2 The diversity of intestinal microbiota of healthy twins and IBD twins is similar, and different from healthy controls.
There is no significant difference in the microbiota alpha diversity between healthy twins and IBD twins in terms of microbiota classification and functional level.

Compared with healthy controls, healthy twins and IBD twins have significantly higher microbial richness (Richness).

At the same time, there was no significant difference in the classification and functional β diversity of the microbiota between healthy twins and IBD twins (PERMANOVA of Bray-Curtis, as shown in Figure 1), but both were different from healthy controls.

Figure 1 There is no significant difference in gut microbial composition (β-diversity) between healthy twins and IBD twins, but both are different from healthy controls.

2.
3 The relationship between IBD consistency, phenotype, zygosity and cohabitation and intestinal microbial composition By comparing the differences in the Bray-Curtis distance between individuals to evaluate IBD consistency, phenotype, zygosity, and cohabitation with individuals during sampling The relationship between the heterogeneity of intestinal microbial composition.

It was found that IBD discordant twins and IBD identical twins did not differ in classification and functional level, which was consistent with the observed similarities in the gut microbial diversity of healthy twins and IBD twins (Figure 2A).

Compared with the unrelated healthy control group, the difference in intestinal microbes from healthy twins to UC and then to CD twins gradually increased, indicating the heterogeneous changes in the composition of intestinal microbes in IBD (Figure 2B).

During the sampling process, the gut microbiota of identical twins, fraternal twins, or twins living together was not more similar to the random healthy control group (Figure 2C, D).

Figure 2 The composition of the gut microbiome of random healthy individuals is more similar to the gut microbiome of IBD coherence, zygosity, or co-living twins.

2.
4 The relative abundance of species and pathways between healthy twins, IBD twins, and unrelated IBD patients are different from those of healthy controls in order to identify whether the gut microbial characteristics of healthy twins are similar to those of IBD twins, unrelated IBD patients or healthy controls Microbiome similarity, multivariate linear regression analysis of IBD subtypes (CD, UC, and no IBD) (age, gender, BMI, use of antibiotics and PPI, depth of sequencing).

In the twin cohort analysis, zygosity and diseased parts were additionally adjusted, and there were no significant differences in species and pathways between IBD twins and healthy twins.

However, compared with healthy controls, the gut microbiota of IBD twins has 19 different species and 105 different pathways, and unrelated IBD patients have 18 different species and 153 different pathways.

There were also significant differences in the relative abundance of 13 microorganisms and 78 pathways in the gut microbiota of healthy twins and healthy controls (Figure 3).

2.
5 Compared with the healthy control group, healthy twins have the same microbial groups and pathways as IBD twins and unrelated IBD patients.
Compared with the healthy control group, there are 19 species and 105 pathways in IBD twins, 8 of which are different The species and 37 pathways also differ among healthy twins.

In addition, among the 18 different species and 153 different pathways between unrelated IBD patients and healthy controls, 1 species and 30 pathways are also different between healthy controls and healthy twins (Figure 3).

Figure 3 The relative abundance of species and pathways of intestinal microbiota of healthy twins, IBD twins and unrelated IBD patients are significantly different from those of healthy controls.

Compared with healthy controls, the relative abundance of potential pathogenic microorganisms such as Escherichiaunclassified, Gordonibacterpamelaeae and Eggerthellaunclassified in healthy twins, IBD twins and unrelated IBD patients increased.

The relative abundance of Faecalibacterium prausnitzii in IBD twins and unrelated IBD patients was increased compared to healthy controls (Figure 4).

Figure 4 The relative abundance of IBD-related species compared with healthy controls, healthy IBD, IBD twins and unrelated IBD patients with Chinese family-specific surface Enterobacter co-antigens (Escherichia), siderophores (enterobactin and aerobicin) The relative abundance of biosynthetic pathways and genes encoding arginine degradation has increased.

Compared with the healthy control group, the degradation pathway of a short-chain fatty acid, propionic acid, was increased in healthy twins and IBD twins.

As the abundance of F.
prausnitzii decreases, the relative abundance of butyrate synthesis pathways in IBD twins and unrelated IBD patients is lower than in healthy controls.

Compared with the healthy control group, the potential pathogenic species and pro-inflammatory pathways in the gut microbiota of healthy twins and IBD inconsistent twins increased (Figure 5).

Figure 5 Relative abundance of IBD-related pathways 3.
Discussion This cross-sectional study analyzed the gut microbiome of IBD twins through metagenomic sequencing, and found the α and β diversity, species and pathways between healthy twins and IBD twins There is no significant difference in the relative abundance of.

Compared with healthy controls matched for age, gender and BMI, healthy twins and IBD twins, as well as unrelated IBD patients, have a large overlap in microbiota species and pathways, and there are IBD-related species and potential inflammation-related pathways.

This indicates that the diagnosis of IBD may be before the change in microbial composition, or the increased risk of IBD is related to the change in microbial composition, or both.

Contrary to the results of the previous study on the microbiome of IBD twins with a small sample size based on 16S sequencing, there was no statistical difference in the relative abundance of microbial groups and pathways between IBD twins and healthy twins in this study.

In order to further reveal the formation process of the intestinal microbiome of IBD twins, patients with unrelated IBD were included in the study.

There are only minor differences in the microbial groups and pathways between unrelated IBD patients and IBD twins.

Healthy twins not only overlap with IBD twins in microbial species and pathways, but also overlap with unrelated IBD patients.

This shows that shared environmental factors and genetic background are not the only explanation for the overlap of microbiota taxa between IBD twins and healthy twins.

An IBD feature of healthy twins is an increase in the relative abundance of unclassified Escherichia.

Previous reports indicate that this unclassified Escherichia is related to UC and CD, and may be a key pathogenic factor for IBD.

In addition, the biosynthetic pathway of family-specific enterobacteria co-antigens is increased in healthy twins, IBD twins and unrelated IBD patients, and this pathway is shared by all bacterial genera of the Enterobacteriaceae family.

Compared with healthy controls, the relative abundance of Fe3þ siderophore, a known toxic factor, in healthy twins, IBD twins, and unrelated IBD patients increased.

In addition, the relative abundance of genes encoding arginine degradation and the degradation of propionic acid (a short-chain fatty acid SCFAs) in healthy twins, IBD twins, and unrelated IBD patients increased.

Arginine is a polyamine (helps the integrity of the intestine and reduces the expression of pro-inflammatory cytokines), while SCFAs are an important source of energy for intestinal epithelial cells, and SCFAs supplementation can reduce colon inflammation.

In summary, the study found that the gut microbiome of healthy twins from IBD discordant twins showed IBD-related characteristics at both the classification and functional level.

The gut microbiota of these individuals is similar to the gut microbiota of their twins with IBD and unrelated IBD patients, but different from the healthy controls.

The characteristics of these IBD-like microbial communities reflect the common genetic background and environment, and may precede the development of IBD.

The IBD-like microbiota characteristics of healthy twins may precede the development of IBD and reflect the genetic composition and environmental factors shared between these individuals, but they do not necessarily lead to the development of IBD.

Therefore, it is necessary to conduct a longitudinal study of multi-time sampling of high-risk populations before the onset of IBD.

 Comment: This study is currently the largest twin cohort study in the field of IBD and microbiome.
It uses a large sample size + metagenomic sequencing method to accurately reveal the IBD-related gut microbiota.

The author carefully compared multiple aspects of overlapping microbiomes in IBD identical and inconsistent twins, healthy people, and unrelated IBD patients, and adjusted the confounding factors through a multivariate linear model.
The rigorous thinking is worth learning.

However, the multiple cohorts in this study may have batch effects due to differences in sampling, sample storage, and DNA extraction methods.

Although there have been many reports on 16S sequencing studies for twin IBD patients, this article can still be published on 17+ Gastroenterology.
With the novel grouping design, the analysis of IBD consistent/inconsistent/co-living twin flora eliminates environmental and dietary effects.
Impact, the addition of patients with unrelated IBD further increased the accuracy of the identification of differential flora.

The results of high-throughput sequencing with large sample sizes are more convincing, and metagenomic sequencing technology can in-depth study of IBD-related differences in bacterial species and functions.

This article also lacks a longitudinal study of the dynamic changes of the microbiota during the development of IBD, which will also be an important research direction in the microbiome field in the next few years.

 References: [1] Brand EC, Klaassen MAY, Gacesa R, Vila AV, Ghosh H, de Zoete MR, Boomsma DI, Hoentjen F, Horjus Talabur Horje CS, van de Meeberg PC and others.
Healthy cotwins sharegut microbiome signatures with their inflammatory bowel disease twins andunrelated patients.
Gastroenterology 2021.
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