scholarly journals Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Sijia Li ◽  
Siyuan Yang ◽  
Yuzheng Zhou ◽  
Cyrollah Disoma ◽  
Zijun Dong ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bifidobacterium Longum ◽  
Enterobacter Aerogenes ◽  
Streptococcus Thermophilus ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Diagnostic Potential ◽  
Prevotella Bivia ◽  
Gi Symptoms ◽  
Species Markers

COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances of gut microbiota have been previously linked to respiratory virus infection. Understanding how the gut–lung axis affects the progression of COVID-19 can provide a novel framework for therapies and management. In this study, we examined the gut microbiota of patients with COVID-19 (n = 47) and compared it to healthy controls (n = 19). Using shotgun metagenomic sequencing, we have identified four microorganisms unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, and Prevotella bivia. The abundances of Bacteroides stercoris, B. vulgatus, B. massiliensis, Bifidobacterium longum, Streptococcus thermophilus, Lachnospiraceae bacterium 5163FAA, Prevotella bivia, Erysipelotrichaceae bacterium 6145, and Erysipelotrichaceae bacterium 2244A were enriched in COVID-19 patients, whereas the abundances of Clostridium nexile, Streptococcus salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes, and Adlercreutzia equolifaciens were decreased (p < 0.05). The relative abundance of butyrate-producing Roseburia inulinivorans is evidently depleted in COVID-19 patients, while the relative abundances of Paraprevotella sp. and the probiotic Streptococcus thermophilus were increased. We further identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules. Notably, 15 optimal microbial markers were identified using the random forest model to have strong diagnostic potential in distinguishing COVID-19. Based on Spearman’s correlation, eight species were associated with eight clinical indices. Moreover, the increased abundance of Bacteroidetes and decreased abundance of Firmicutes were also found across clinical types of COVID-19. Our findings suggest that the alterations of gut microbiota in patients with COVID-19 may influence disease severity. Our COVID-19 classifier, which was cross-regionally verified, provides a proof of concept that a set of microbial species markers can distinguish the presence of COVID-19.

scholarly journals Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

scholarly journals Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients

2020 ◽  
Vol 4 (22) ◽  
pp. 5797-5809
Author(s):  
Emma E. Ilett ◽  
Mette Jørgensen ◽  
Marc Noguera-Julian ◽  
Jens Christian Nørgaard ◽  
Gedske Daugaard ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Diversity ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Clinical Factors ◽  
Hematopoietic Stem ◽  
Lower Abundance ◽  
Shotgun Metagenomic Sequencing ◽  
Stool Samples ◽  
Gene Richness

Abstract Acute graft-versus-host disease (aGVHD) is a leading cause of transplantation-related mortality after allogeneic hematopoietic stem cell transplantation (aHSCT). 16S ribosomal RNA (16S rRNA) gene-based studies have reported that lower gut bacterial diversity and the relative abundance of certain bacteria after aHSCT are associated with aGVHD. Using shotgun metagenomic sequencing and a large cohort, we aimed to confirm and extend these observations. Adult aHSCT recipients with stool samples collected from day −30 to day 100 relative to aHSCT were included. One sample was selected per patient per period (pre-aHSCT (day −30 to day 0), early post-aHSCT (day 1 to day 28), and late post-aHSCT (day 29 to day 100)), resulting in 150 aHSCT recipients and 259 samples. Microbial and clinical factors were tested for differences between time periods and an association with subsequent aGVHD. Patients showed a decline in gut bacterial diversity posttransplant, with several patients developing a dominance of Enterococcus. A total of 36 recipients developed aGVHD at a median of 34 days (interquartile range, 26-50 days) post-aHSCT. Lower microbial gene richness (P = .02), a lower abundance of the genus Blautia (P = .05), and a lower abundance of Akkermansia muciniphila (P = .01) early post-aHSCT was observed in those who developed aGVHD. Myeloablative conditioning was associated with aGVHD along with a reduction in gene richness and abundance of Blautia and A muciniphila. These results confirm low diversity and Blautia being associated with aGVHD. Crucially, we add that pretransplant conditioning is associated with changes in gut microbiota. Investigations are warranted to determine the interplay of gut microbiota and conditioning in the development of aGVHD.

scholarly journals P053 Overabundance of Lactobacillus species in gut microbiota of IBD patients

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S160-S161
Author(s):  
D Khusnutdinova ◽  
M Markelova ◽  
M Siniagina ◽  
E Boulygina ◽  
S Abdulkhakov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Active Phase ◽  
Bioinformatic Analysis ◽  
Lactobacillus Species ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Inflammatory Bowel ◽  
Stool Samples

Abstract Background Changes in the composition of gut microbiota, and their metabolic pathways, are important factors in the pathogenesis of inflammatory bowel disease (IBD). Many clinical trials have shown that taking probiotics based on Lactobacillus has a positive effect on patients with IBD. However, Lactobacillus should be used more carefully during the active phase of IBD, since some strains can negatively affect the pathogenesis of the disease1,2. The aim of this study was to assess the diversity of Lactobacillus species in the gut microbiome of IBD patients and healthy volunteers. Methods In the study, 62 stool samples from healthy people, 31 from patients with Crohn’s disease (CD), and 34 - ulcerative colitis (UC) in active phase were analyzed. DNA was isolated using the QIAamp Fast DNA Stool Mini Kit (Qiagen, USA) following with shotgun metagenomic sequencing the NextSeq 500 (project #0671-2020-0058). Bioinformatic analysis was performed with the MetaPhlAn2 package. Results An increased relative abundance of Lactobacillus was found in patients with IBD (3.2% ± 6.6% in CD and 1.6% ± 2.8 in UC) compared to healthy individuals (0.3% ± 1.2%, p<0.05). In the control group, Lactobacillus were absent in 41% of samples and 1–5 species were found in 58% of samples. Most CD and UC patients are characterized by the presence of 3 to 5 species of Lactobacillus (38% and 31%, respectively). For 23% of CD patients and 26% of UC patients, 6 to 9 types of Lactobacillus were found. Some patients with IBD have more than 10 different types of Lactobacillus in the gut microbiota (Fig.1). The intestinal microbiota in IBD patients is characterized by an increased abundance of several species: L. salivarius, L. gasseri, L. mucosae, as well as L. casei paracasei in patients with CD and L. vaginalis in patients with UC (Fig.2). Conclusion The composition of the intestinal microbiota of IBD patients differs significantly in terms of Lactobacillus proportion and species diversity. Overabundance of five Lactobacillus species could be associated with the active phase of IBD. References

scholarly journals Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Runbiao Wu ◽  
Luyu Wang ◽  
Jianping Xie ◽  
Zhisheng Zhang
Keyword(s):  
Gut Microbiota ◽  
Wolf Spider ◽  
Metagenomic Sequencing ◽  
Wolf Spiders ◽  
Shotgun Metagenomics ◽  
Microbial Genomes ◽  
Shotgun Metagenomic Sequencing ◽  
Crucial Component ◽  
Genes Encoding ◽  
And Function

Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.5% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.

scholarly journals Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes

2021 ◽  
Author(s):  
Lauren Tso ◽  
Kevin S Bonham ◽  
Alyssa Fishbein ◽  
Sophie Rowland ◽  
Vanja Klepac-Ceraj ◽  
...  
Keyword(s):  
Human Milk ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Species Group ◽  
Human Breast Milk ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Specific Primers ◽  
Breastfed Infants ◽  
Shotgun Metagenomic Sequencing

Bifidobacterium longum subsp. infantis (B. infantis) is one of few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis, by molecular methods. These two organisms are classified in the same species group as B. infantis but do not share the ability to metabolize human milk oligosaccharides (HMOs). Here, we compared HMO-metabolizing genes across different Bifidobacterium genomes to develop B. infantis specific primers and determine if they alone can be used to quickly characterize B. infantis with shotgun metagenomic sequencing data. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, used this characterization to test for its prevalence in infants, and validated the results using the B. infantis-specific primers. By examining stool samples from a cohort of US children and pregnant women using shotgun metagenomic sequencing, we observed that only 18 of 204 (8.8%) of children under 2 years old harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.

scholarly journals Domestication Shapes the Community Structure and Functional Metagenomic Content of the Yak Fecal Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Haibo Fu ◽  
Liangzhi Zhang ◽  
Chao Fan ◽  
Chuanfa Liu ◽  
Wenjing Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Short Chain Fatty Acids ◽  
Fecal Microbiota ◽  
Glycoside Hydrolase Family ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Rdna Sequencing ◽  
Key Factor ◽  
Methane Metabolism ◽  
Hydrolase Family

Domestication is a key factor of genetic variation; however, the mechanism by which domestication alters gut microbiota is poorly understood. Here, to explore the variation in the structure, function, rapidly evolved genes (REGs), and enzyme profiles of cellulase and hemicellulose in fecal microbiota, we studied the fecal microbiota in wild, half-blood, and domestic yaks based on 16S rDNA sequencing, shotgun-metagenomic sequencing, and the measurement of short-chain-fatty-acids (SCFAs) concentration. Results indicated that wild and half-blood yaks harbored an increased abundance of the phylum Firmicutes and reduced abundance of the genus Akkermansia, which are both associated with efficient energy harvesting. The gut microbial diversity decreased in domestic yaks. The results of the shotgun-metagenomic sequencing showed that the wild yak harbored an increased abundance of microbial pathways that play crucial roles in digestion and growth of the host, whereas the domestic yak harbored an increased abundance of methane-metabolism-related pathways. Wild yaks had enriched amounts of REGs in energy and carbohydrate metabolism pathways, and possessed a significantly increased abundance of cellulases and endohemicellulases in the glycoside hydrolase family compared to domestic yaks. The concentrations of acetic, propionic, n-butyric, i-butyric, n-valeric, and i-valeric acid were highest in wild yaks. Our study displayed the domestic effect on the phenotype of composition, function in gut microbiota, and SCFAs associated with gut microbiota, which had a closely association with the growth performance of the livestock. These findings may enlighten the researchers to construct more links between economic characteristics and gut microbiota, and develop new commercial strains in livestock based on the biotechnology of gut microbiota.

scholarly journals Yoghurt consumption is associated with transient changes in the composition of the human gut microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10 -10 ) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10 -12 ) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10 -8 ) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LL-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation. Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species ( i.e. S. thermophilus and B. lactis ).

Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in major depressive disorder patients

2019 ◽  
pp. 1-12 ◽  
Author(s):  
Wen-tao Lai ◽  
Wen-feng Deng ◽  
Shu-xian Xu ◽  
Jie Zhao ◽  
Dan Xu ◽  
...  
Keyword(s):  
Major Depressive Disorder ◽  
Gut Microbiota ◽  
Depressive Disorder ◽  
Characteristic Curve ◽  
Critical Role ◽  
Metagenomic Sequencing ◽  
Major Depressive ◽  
Shotgun Metagenomics ◽  
Shotgun Metagenomic Sequencing ◽  
Tryptophan Pathway

Abstract Background The microbiota–gut–brain axis, especially the microbial tryptophan (Trp) biosynthesis and metabolism pathway (MiTBamp), may play a critical role in the pathogenesis of major depressive disorder (MDD). However, studies on the MiTBamp in MDD are lacking. The aim of the present study was to analyze the gut microbiota composition and the MiTBamp in MDD patients. Methods We performed shotgun metagenomic sequencing of stool samples from 26 MDD patients and 29 healthy controls (HCs). In addition to the microbiota community and the MiTBamp analyses, we also built a classification based on the Random Forests (RF) and Boruta algorithm to identify the gut microbiota as biomarkers for MDD. Results The Bacteroidetes abundance was strongly reduced whereas that of Actinobacteria was significantly increased in the MDD patients compared with the abundance in the HCs. Most noteworthy, the MDD patients had increased levels of Bifidobacterium, which is commonly used as a probiotic. Four Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K01817, K11358, K01626, K01667) abundances in the MiTBamp were significantly lower in the MDD group. Furthermore, we found a negative correlation between the K01626 abundance and the HAMD scores in the MDD group. Finally, RF classification at the genus level can achieve an area under the receiver operating characteristic curve of 0.890. Conclusions The present findings enabled a better understanding of the changes in gut microbiota and the related Trp pathway in MDD. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing MDD patients form HCs.

scholarly journals Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

2019 ◽  
Author(s):  
Anuradha Ravi ◽  
Fenella D Halstead ◽  
Amy Bamford ◽  
Anna Casey ◽  
Nicholas M. Thomson ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Patient Specific ◽  
Metagenomic Sequencing ◽  
Icu Patients ◽  
Adult Intensive Care Unit ◽  
Shotgun Metagenomic Sequencing ◽  
Health And Disease ◽  
Genome Analyses ◽  
Phylogenetic Profiling

AbstractBackgroundFor long-stay patients on the adult intensive care unit, the gut microbiota plays a key role in determining the balance between health and disease. However, it remains unclear which ICU patients might benefit from interventions targeting the gut microbiota or the pathogens therein.MethodsWe undertook a prospective observational study of twenty-four ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses.ResultsTwo-thirds of patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of <4) at some stage during their stay in ICU, often accompanied by absence or loss of beneficial commensal bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but administration of other antibiotics, including piperacillin-tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission ofEnterococcus faecium. In some patients we also saw domination of the gut microbiota by commensal organisms, such asMethanobrevibacter smithii.ConclusionsOur results support a role for metagenomic surveillance of the gut microbiota and pave the way for patient-specific interventions that maintain or restore gut microbial diversity in the ICU.

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