AB0824 ANALYSIS OF GUT MICROBIOTA IN RHEUMATOID ARTHRITIS PATIENTS

Background:Gastrointestinal microbiota, particularly gut microbiota is an indispensable environmental factor in the progression of Rheumatoid Arthritis (RA). Understanding the diversity and function of the intestinal flora in patients with RA is part and parcel to understand the relationship between microbiota and human health.Objectives:This study aimed to identify the diversity and function of the intestinal flora in patients with RA.Methods:A total of 166 participants were recruited in this study, comprising 93 RA patients and 73 age and sex-matched healthy controls (HCs). Microbial genome was extracted from approximately 250mg fresh fecal samples from all participants using QIAamp PowerFecal DNA Kit (Qiagen). The V3-V4 variable regions of bacterial 16S rRNA genes were sequenced with the Illumina Miseq PE300 system. Sequence data were compiled and processed using Qiime2. Sequences were grouped into operational taxonomic units (ASVs)1. Microbial diversity was estimated by the Simpson index. PICRUSt2 was used to predict KEGG functional pathway differences between RA and HC intestinal flora functions based on ASV Tables2. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis was performed using LEfSe software to discovery the different intestinal flora and functions between RA and healthy.Results:The alpha-diversity index of Simpson the microbiome in RA patients was lower than that of HCs (Figure 1a, P <0.05). Compared with HCs, bacterial Bacilli and Lactobacillales were more abundant in patients with RA (Figure 1b, P <0.05). In contrast, Marinifilaceae, Peptococcaceae, Peptococcales and Phascolarcto bacterium were less abundant in the RA group (Figure 1b, P <0.05). As shown in Figure 1c, propanoate metabolism, taurine and hypotaurine metabolism, ascorbate and aldarate metabolism, biosynthesis of siderophore group nonribosomal peptides and glutathione metabolism were the most significantly altered pathways in RA (P <0.05). Epithelial cell signaling in Helicobacter pylori infection, RNA transport, RNA degradation and plant-pathogen interaction were the most significantly altered pathways in HC (P <0.05). The different KEGG metabolic pathways were mainly concentrated in carbohydrate and amino acid metabolism.Conclusion:Gut dysbiosis in RA patients mainly characterized by reduced the diversity and impaired abundance of the intestinal flora, which severely influence the metabolism of gastrointestinal microbiota. The discovery of the associated intestinal microbiota of RA may provide a new idea for RA treatment.References:[1]Han L, Zhao K, Li Y, et al. A gut microbiota score predicting acute graft-versus-host disease following myeloablative allogeneic hematopoietic stem cell transplantation. Am J Transplant 2020;20(4):1014-27. doi: 10.1111/ajt.15654 [published Online First: 2019/10/13][2]Liss MA, White JR, Goros M, et al. Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer. Eur Urol 2018;74(5):575-82. doi: 10.1016/j.eururo.2018.06.033 [published Online First: 2018/07/17]Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

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Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark

Genome Medicine ◽

10.1186/s13073-021-00851-9 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Nishal Kumar Pinna ◽

Ranjit Mohan Anjana ◽

Shruti Saxena ◽

Anirban Dutta ◽

Visvanathan Gnanaprakash ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Large Scale ◽

Negative Binomial ◽

Intestinal Inflammation ◽

Cohort Effect ◽

16S Rrna Genes ◽

Rrna Genes ◽

Low Grade ◽

Variable Regions

Abstract Background Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of “prediabetic” (PD) subjects has not been reported. Identifying robust gut microbiome signatures of prediabetes and characterizing early prediabetic stages is important for the understanding of disease development and could be crucial in early diagnosis and prevention. Methods The current study performed amplification and sequencing on the variable regions (V1–V5) of the 16S rRNA genes to profile and compare gut microbiota of prediabetic individuals (N = 262) with normoglycemic individuals (N = 275) from two cohorts in India and Denmark. Similarly, fasting serum inflammatory biomarkers were profiled from the study participants. Results After correcting for strong country-specific cohort effect, 16 operational taxonomic units (OTUs) including members from the genera Prevotella9, Phascolarctobacterium, Barnesiella, Flavonifractor, Tyzzerella_4, Bacteroides, Faecalibacterium, and Agathobacter were identified as enriched in normoglycaemic subjects with respect to the subjects with prediabetes using a negative binomial Wald test. We also identified 144 OTUs enriched in the prediabetic subjects, which included members from the genera Megasphaera, Streptococcus, Prevotella9, Alistipes, Mitsuokella, Escherichia/Shigella, Prevotella2, Vibrio, Lactobacillus, Alloprevotella, Rhodococcus, and Klebsiella. Comparative analyses of relative abundance of bacterial taxa revealed that the Streptococcus, Escherichia/Shigella, Prevotella2, Vibrio, and Alloprevotella OTUs exhibited more than fourfold enrichment in the gut microbiota of prediabetic subjects. When considering subjects from the two geographies separately, we were able to identify additional gut microbiome signatures of prediabetes. The study reports a probable association of Megasphaera OTU(s) with impaired glucose tolerance, which is significantly pronounced in Indian subjects. While the overall results confirm a state of proinflammation as early as in prediabetes, the Indian cohort exhibited a characteristic pattern of abundance of inflammatory markers indicating low-grade intestinal inflammation at an overall population level, irrespective of glycemic status. Conclusions The results present trans-ethnic gut microbiome and inflammation signatures associated with prediabetes, in Indian and Danish populations. The identified associations may be explored further as potential early indicators for individuals at risk of dysglycemia.

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VASCULAR WALL CONDITION, GUT MICROBIOTA COMPOSITION, AND DIET IN PATIENTS WITHOUTCARDIOVASCULAR DISEASES

Clinical Practice ◽

10.17816/clinpract7362-72 ◽

2016 ◽

Vol 7 (3) ◽

pp. 62-72

Author(s):

D A Kashtanova ◽

O N Tkacheva ◽

L V Egshatyan ◽

E V Plokhova ◽

A S Popenko ◽

...

Keyword(s):

Gut Microbiota ◽

Program Analysis ◽

Subclinical Atherosclerosis ◽

Vascular Wall ◽

16S Rrna Genes ◽

Rrna Genes ◽

Microbiota Composition ◽

Variable Regions ◽

Wall Stiffness ◽

Gut Microbiota Composition

Purpose of the study. To study the relationship between the gut microbiota composition, the state of the vascular wall and nutrient intake in patients without clinical manifestation of cardiovascular disease.Materials and methods. The study included 92 residents from Moscow and the Moscow region, men and women aged 25 to 76 y.o., without clinical manifestations of chronic diseases, with no medical treatment but with possible presence of cardiovascular risk factors. All the participants were examined with duplex scanning of the carotid arteries with the definition of the thickness of the intima-media complex (IMC), the presence of atherosclerotic plaques, measuring carotid-femoral pulse wave velocity (PWV), the measurement of interleukin-6 (IL-6) and C-reactive protein (C-RP) and sequencing of the V3-V4 variable regions of 16S rRNA genes of the gut microbiota.Diet was studied by quantitative assessment of consumer products using a standardized computer program «Analysis of Human Nutrition states» (version 1.2.4 Research Institute of Nutrition 2003-2006).Results. The study revealed that in the investigated cohort IMC thickness was greater in those with a large number of bacterial genera Serratia and Blautia. Bifidobacterium representation was increased and Blautia representation was decreased in those who consumed a lot of starch.Conclusion. The composition of the gut microbiota is associated with both vascular wall stiffness and atherosclerosis. In addition, the bacteria associated with subclinical atherosclerosis were more represented among those who consumed smaller amounts of complex carbohydrates.

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Microflora Disturbance during Progression of Glucose Intolerance and Effect of Sitagliptin: An Animal Study

Journal of Diabetes Research ◽

10.1155/2016/2093171 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 28

Author(s):

Xinfeng Yan ◽

Bo Feng ◽

Peicheng Li ◽

Zhaosheng Tang ◽

Lin Wang

Keyword(s):

Gut Microbiota ◽

Glucose Intolerance ◽

Intestinal Flora ◽

Diabetic Rats ◽

16S Rrna Genes ◽

Rrna Genes ◽

Fecal Dna ◽

Dipeptidyl Peptidase 4 ◽

Beneficial Effects ◽

Dipeptidyl Peptidase 4 Inhibitor

Background. Emerging evidences have shown a close interplay between obesity, diabetes, and intestinal flora disturbance. Dipeptidyl peptidase-4 inhibitor, exemplified by sitagliptin, is highly efficacious in treating type 2 diabetes (T2DM), yet little is known if sitagliptin exerts beneficial effects on microbiota associated with obesity and T2DM. We evaluated changes of gut microbiota following the induction of obesity and T2DM in a streptozotocin treated high fat/high carbohydrate fed (HF/HC-STZ) rat model and explored the effect of sitagliptin on gut microbiota for HF/HC-STZ rats.Methods. Sitagliptin was administered via oral gavage to diabetic rats. Fecal DNA extraction and 454 pyrosequencing based on analysis of 16S rRNA genes was utilized to determine the overall structure of microbiota in fecal DNA samples.Results. Results showed that, at the level of phylum, there was higher abundance of Firmicutes and Tenericutes and less abundance of Bacteroidetes in obese rats compared to their lean counterparts. At the level of genus, short-chain fatty acid- (SCFA-) producing bacteria,Blautia,Roseburia, andClostridium, and probioticsLactobacillus,Bifidobacterium, and so forth were identified significantly different from each other among conditions.Conclusion. Marked shifts of the gut microbiota structure were observed in the rats during development of glucose intolerance. Intestinal flora changed in the process of glucose intolerance, and treatment of sitagliptin moderately corrected the dysbiosis of microbiota in T2DM.

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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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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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Bacterial Diversity and Function of Aerobic Granules Engineered in a Sequencing Batch Reactor for Phenol Degradation

Applied and Environmental Microbiology ◽

10.1128/aem.70.11.6767-6775.2004 ◽

2004 ◽

Vol 70 (11) ◽

pp. 6767-6775 ◽

Cited By ~ 98

Author(s):

He-Long Jiang ◽

Joo-Hwa Tay ◽

Abdul Majid Maszenan ◽

Stephen Tiong-Lee Tay

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Bacterial Diversity ◽

Sequencing Batch Reactor ◽

Batch Reactor ◽

Phenol Degradation ◽

16S Rrna Genes ◽

Rrna Genes ◽

Aerobic Granules ◽

And Function

ABSTRACT Aerobic granules are self-immobilized aggregates of microorganisms and represent a relatively new form of cell immobilization developed for biological wastewater treatment. In this study, both culture-based and culture-independent techniques were used to investigate the bacterial diversity and function in aerobic phenol- degrading granules cultivated in a sequencing batch reactor. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes demonstrated a major shift in the microbial community as the seed sludge developed into granules. Culture isolation and DGGE assays confirmed the dominance of β-Proteobacteria and high-G+C gram-positive bacteria in the phenol-degrading aerobic granules. Of the 10 phenol-degrading bacterial strains isolated from the granules, strains PG-01, PG-02, and PG-08 possessed 16S rRNA gene sequences that matched the partial sequences of dominant bands in the DGGE fingerprint belonging to the aerobic granules. The numerical dominance of strain PG-01 was confirmed by isolation, DGGE, and in situ hybridization with a strain-specific probe, and key physiological traits possessed by PG-01 that allowed it to outcompete and dominate other microorganisms within the granules were then identified. This strain could be regarded as a functionally dominant strain and may have contributed significantly to phenol degradation in the granules. On the other hand, strain PG-08 had low specific growth rate and low phenol degradation ability but showed a high propensity to autoaggregate. By analyzing the roles played by these two isolates within the aerobic granules, a functional model of the microbial community within the aerobic granules was proposed. This model has important implications for rationalizing the engineering of ecological systems.

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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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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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The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons

Molecular Biology International ◽

10.1155/2014/548683 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 9

Author(s):

Ingo C. Starke ◽

Wilfried Vahjen ◽

Robert Pieper ◽

Jürgen Zentek

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Dna Extraction ◽

16S Rrna Genes ◽

Read Length ◽

Rrna Genes ◽

Rrna Gene ◽

Variable Regions ◽

Extraction Procedures ◽

Primer Sets

In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns) and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r) were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2×105 sequences were used for analysis after processing for read length (150 bp), minimum sequence occurrence (5), and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

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Effects of Waterlogging on Soybean Rhizosphere Microbial Community Profiled Using Illumina MiSeq, LoopSeq, and PacBio 16S rRNA Genes Sequences

10.21203/rs.3.rs-702861/v1 ◽

2021 ◽

Author(s):

Yu TaoBing ◽

Cheng Lang ◽

Liu Qi ◽

Wang ShaSha ◽

Zhou Yuan ◽

...

Keyword(s):

16S Rrna ◽

Crop Yields ◽

Full Length ◽

16S Rrna Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Microbial Structure ◽

Variable Regions ◽

Waterlogging Stress ◽

Rrna Sequencing

Abstract Background: Waterlogging on the global environment has led to a significant decline in crop yields. However, the response of plant-associated microbes to waterlogging stress on different soils is not known. Moreover, there are few reports on whether this response is influenced by different sequencing methods. In this study, the effects of waterlogging on soybean rhizosphere microbial structure on two types of soil were examined, using a short reading 16S rRNA sequencing variable region V4 and two full-length 16S rRNA sequencing variable regions V1-V9.Results: The results revealed some similarities and differences in three sequencing methods for soybean rhizosphere microbial response to waterlogging stress. Based on CPCoA analysis, all the sequencing methods showed that waterlogging on both types of soil significantly affected the bacterial community structure of the soybean rhizosphere, and increased the relative abundance of Geobacter. However, the full-length sequencing methods had higher classification resolution than short-read sequencing (except phylum level of all sequencing methods and class level of LoopSeq sequencing). Further, analysis on OTU level and network showed that waterlogging increased the abundance of some microorganisms related to nitrogen cycle using V4 sequencing, and microorganisms related to phosphorus cycling when using two full-length sequencing methods. This is in line with the core microbial analysis. Environmental factors affecting the structure of microbial communities differed among sequencing methods.Conclusions: In summary, this piece of work detected the effects of waterlogging on soybean rhizosphere microbes using three sequencing methods. Some functional microbes were enriched in the rhizosphere, which may benefit soybean in resisting waterlogging stress. On the other hand, there were several differences in results among the three sequencing methods which might affect the response of rhizosphere microbial structure to stress. Our analysis of sequencing methods on various levels provides some useful information on environmental samples sequencing.

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