metagenomic analysis of human gut microbiome

Rev. doi: 10.1128/mSphere.00227-21. These are related to fatty acid metabolism and the upstream part of the biotin synthesis pathway provides a long-chain acyl as the starting point for the biosynthesis. Google Scholar. Li X, Wu J, Kang Y, Chen D, Chen G, Zeng X, Wang J. In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis. 8600 Rockville Pike Although none of these studies provided diet information for the samples, it would be reasonable to speculate that the observed differences could be a diet-dependent effect (based on Western and non-Western diets). Oncol. Before vitamin genes related to biosynthesis or transporters or both. The .gov means its official. The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. Unable to load your collection due to an error, Unable to load your delegates due to an error, The left panel denotes the significant Spearman correlations (FDR. The https:// ensures that you are connecting to the Bacterial structure and dynamics in mango (Mangifera indica) orchards after long term organic and conventional treatments under subtropical ecosystem. USA, China, Denmark, Spain) under different states of health and disease. Clin. It is worth noting that, the results show that enriched levels of Retinol metabolism in BFVD groups, with implications in several essential developmental processes such as vision, bone, and teeth (Table S7). However, except Actinobacteria and Bacteroidetes, there were no significant differences in relative abundance of Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, and Fusobacteria between two groups. Science 359(6371), 97103 (2018). Clin. Nair, R. & Maseeh, A. Vitamin D: the sunshine vitamin. Disclaimer, National Library of Medicine Linear regression results of abundance of Bifidobacterium and circulating vitamin D level. PLoS Biol. It is worth noting that a significant correlation between the proportion of Bifidobacterium and BFVD group, almost all the samples in the group contain a higher proportion of Bifidobacterium than non-VD group, the proportion of Bifidobacterium in BFVD and BFCT were 51.6% and 44.2% of average, respectively. To better reveal the differences of the microbial communities among the different time points, Principal Coordinate Analysis (PCoA) of unweighted UniFrac79 distances was performed to assess the beta diversity of communities. Nat. Microbiome Analyses The HMP performed 16S rRNA and metagenomic sequencing of samples from a healthy human population to address questions such as whether there is a "core" microbiome at individual body sites and whether variation in the microbiome can be systematically studied. Pediatr. The inter-individual variation of microbial composition and function profile, Fig. In addition, one-way analysis of similarity (non-parametric test ANOSIM) was performed to test for statistically significant differences between the metagenomic profiles and p-values<0.05 were considered to be significant. Int. Laursen, M. F. et al. Curr. Davidson RT, Foley AL, Engelke JA, Suttie JW. Dominguez-Bello, M. G. et al. and transmitted securely. For the Chinese cohort (Fig. CAS Immunol. We focused on vitamin metabolism of human gut microbiota as it might be conserved across distantly related microbial species, potentially because they are an integral part of the carbon metabolic network. Integr. Color key for correlation is shown. Of total 7021 possible pairs of species combinations (171 species (675 strains) considered), 2030 (i.e. (Rio J.) Before Endocrinol. Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics. The Human Microbiome Project Consortium. 2022 Mar;42(3):403-412. doi: 10.1007/s00296-021-05007-x. Based on the presence or absence of genes encoding proteins required in vitamin biosynthetic pathways or transporter mechanisms or both, each microbial species was assigned as either vitamin prototrophs (producers) or vitamin consumers (consumers) or producer-consumer (dual) respectively for every vitamin type. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. From PRJEB2054, 14 and 25 samples were of healthy controls and IBD subjects from Spain respectively [19]. Provided by the Springer Nature SharedIt content-sharing initiative. NCI CPTC Antibody Characterization Program, Baker BJ, Sheik CS, Taylor CA, et al. ; (iii) Based on the classification of microbial species, as vitamin producers or consumers or both, what type of species pair are correlated predominantly? Taxonomic distribution of bacterial communities in fecal samples from breastfed infants with vitamin D supplementation. These findings suggest that it is not only the difference in species abundance that sets two groups apart, it is also the functional features of the abundant species that contributes to determining a healthy gut microbiome. Data table with relative abundance of species and metatranscriptomics data for the HMP2 cohort were obtained from their publicly available project website [14]. Family level taxonomic composition correlated with the number of OTUs identified by Mg-Rast and QIIme. We thank our research engineers Pierre-Etienne Cholley and Petre Mihail Anton for their computational support. Several methods for taxonomic classification of bacterial sequences are discussed. Cite this article. 2021 Jul;186:106235. doi: 10.1016/j.mimet.2021.106235. Federal government websites often end in .gov or .mil. -, Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Succession of microbial consortia in the developing infant gut microbiome. In Vitamin D (ed. Curr. Koenig, J. E. et al. This conservation could also be due to the limited number of reactions involved in riboflavin pathway compared to other pathways. 5. (Encinitas) 13(6), 1722 (2014). It was found that the plasma PFOS levels were lower in inulin-fed mice, and there was a trend of lower liver accumulation of PFOS in soluble fiber-fed mice compared with the control group. 8(4), 461467 (2016). Rep. 3(1), 7581 (2016). The DNA was eluted with Buffer AE and centrifuged, after which the DNA extract was stored at20C until further analysis. 16(1), 4147 (2009). Microbiome Analysis Reveals Diversity and Function of. analyzed the results. The x-axis represents the reaction IDs associated to each vitamin pathway and on the y-axis the list of abundant gut bacteria are shown. Article The version 1.9.1 of the Quantitative Insights Into Microbial Ecology (QIIME)69 pipeline (http://qiime.org/index.html) was applied for sequence quality assessment with the quality threshold is 19 (it meant Q20) and the ratio of mismatch is less than 10%. An official website of the United States government. Using the species abundance values, spearman correlation was applied to estimate correlations in determining the relationship between different microbial species. Federal government websites often end in .gov or .mil. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. Or in other words, the summation of the normalized abundances of each vitamins KO in each sample was defined as the total normalized abundance for each vitamin pathway. 106(1), 276283 (2017). After quality filtering, resulted in 20,163,971 (average 83.1%) sequencing reads which used for further analysis. Gout-associated microbial gene functions related. Based on this, we categorized 171 microbial species as Producer (P), Consumer (C) and Producer-Consumer (Dual) for three specific vitamins (biotin, cobalamin, and thiamine) in the following analysis. Dietary intake is one of the major determinants of health, it has been commonly assumed that breast milk is the ideal food for infants by providing the combination of essential nutrients; however, vitamin D in breast milk is often not enough to supply the nutrition need for infants31,32. An official website of the United States government. Iozzo, P. & Sanguinetti, E. Early dietary patterns and microbiota development: still a way to go from descriptive interactions to health-relevant solutions. See this image and copyright information in PMC. GUID:C5147EC6-3EC7-4B60-997A-5C16F8253D91, GUID:B5578CBF-E3BA-4E5B-A391-04C9877515FF, GUID:382F3214-8BAF-4ACF-8A45-4B48AF4DF91C, GUID:3BD1CA6D-453F-4C4A-BC2A-91B48347CA40, GUID:F404B93E-8577-49C5-9B4E-F814407A45F3, GUID:FC6C3B1E-0883-4209-9EF5-7789EF637204, GUID:108C326E-1148-4ACA-8A51-FD61CED38257, B-vitamins, Gut metabolism, Metagenomics, Metatranscriptomics, Vitamin prototrophs, Vitamin consumers. J. Environ. Azad, M. B. et al. 4(12), e413 (2006). Mndez-Salazar EO, Vzquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, ubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martnez-Flores K, Fernndez-Torres J, Lozada-Prez C, Pineda C, Snchez-Gonzlez A, Silveira LH, Burguete-Garca AI, Orbe-Orihuela C, Lagunas-Martnez A, Vazquez-Gomez A, Lpez-Reyes A, Palacios-Gonzlez B, Martnez-Nava GA. Mol Med. 3. We found that the alpha diversity index strongly reduced in infants during the period from birth to term age, while have no obvious change after 1month (Fig. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. Gout metagenomes significantly differed from those of healthy controls. The funding body did not have any role in the study design, data collection, analysis and interpretation, the writing of the manuscript, or any influence on the content of the manuscript. Here we performed a metagenome analysis on 307 fecal samples from 102 gout patients and 86 healthy controls. 1. Collected fecal samples were stored in a -80 freezer before sequencing. Finally, metagenomics data were analyzed in combination with clinical variables to determine potential associations between gut microbiome and HIV-1 infection. The results suggested that gene abundances from T2D subjects in China (as a diagnosed variable) showed an association for vitamin metabolism (F-statistic, p<0.01), while the gene abundances from IBD subjects from USA and Spain showed no significant association with disease status. The relative abundances of Prevotella, Fusobacterium, and Bacteroides were increased in gout, whereas those of Enterobacteriaceae and butyrate-producing species were decreased. 2019;71:991999. Suffixes that end with -B and -T are related to biosynthetic and transporter related genes respectively. Best Pract. CAS In contrast, the genus Bacteroides was observed with lower abundances in the BFVD group instead of pure breastfed infants without vitamin D supplementation (7.9% vs. 15.4%). Routy, B. et al. 2017;7(6):188798. However, it is not clear yet whether the role of vitamin D in the infant gut microbiota. Microbiol. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. sharing sensitive information, make sure youre on a federal Detailed clinical information for the samples is available in the supplemental information of the original article [13]. Science 359(6371), 104108 (2018). Phyla distribution in the studied dataset as computed by each tool. These authors contributed equally: Wei-Te Lei and Kai-Yao Huang. Gut Microbes 3(3), 203220 (2012). Otherwise, vitamin D plays an important role in both the immune and cardiovascular systems, it is considered to be a kind of steroid hormone6. Google Scholar. Meanwhile, the F/B ratio was significantly negatively correlated with BMI at 4-month-old of age, especially in FFI groups as shown in Fig. HHS Vulnerability Disclosure, Help PubMed 2022 Jan-Dec;14(1):2135963. doi: 10.1080/19490976.2022.2135963. The main reasons for low level of vitamin D in children are without supplementary feeding and lack of outdoor sun exposure15. containing genes for both biosynthesis and transport of the same vitamin) contributed to a notable fraction of positive correlations among the possible phenotypes (Additional file 4: Figure S3). Crit. Other recent studies have also suggested the diet and dietary supplements can influence the gut microbiota composition, thereby changing the activity of gut microbiota and linking with obesity traits39,40,41. BMC Microbiol. Median serum concentration of 25-hydroxyvitamin D (25(OH)D) were 16.6 nanograms/milliliter (ng/mL) at the birth and 36.1 at 4-month-old of age. Gulyaeva A, Garmaeva S, Kurilshikov A, Vich Vila A, Riksen NP, Netea MG, Weersma RK, Fu J, Zhernakova A. Lima J, Manning T, Rutherford KM, Baima ET, Dewhurst RJ, Walsh P, Roehe R. J Microbiol Methods. Pettifor, J. M., Thandrayen, K. & Thacher, T. D. Vitamin D Deficiency and Nutritional Rickets in Children. Breastfeed. In Fig. Interestingly, the results showed that the first transition of the gut microbiota in BFIs were earlier than in FFIs. BJOG 123(6), 983993 (2016). ADS Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases. Predicting metagenomic function based on the KEGG database by PICRUSt, a total of 23 KEGG metabolism pathway were predicted across all samples of the two compared groups (Fig. 127(3), 245249 (2008). Charoenngam, N., Shirvani, A. The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions Here we identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. Comparison of relative abundances of microbial taxabetween breast- and formula-fed infants. PB performed the metabolic reconstructions. This is in agreement with the results of [31] who found that bacteria evolve and respond according to environmental changes. Richness of human gut microbiome correlates with metabolic markers. ADS Microbiota of Cow's Milk with Udder Pathologies. Sci Rep 11, 2856 (2021). Our study reveals the country-specific differences between healthy and disease (i.e., T2D and IBD) subjects for at least some of vitamin biosynthetic pathways, which highlights the role of diet and lifestyle in the correlation between human gut microbiota and the health status of the host. Kim J, Kim MS, Koh AY, Xie Y, Zhan X. FMAP: functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies. Pairwise comparisons using MannWhitney test. Google Scholar. Fig. Bifidobacterium, the probiotics can secrete the antimicrobial compounds and metabolites to fight against the various diseases and gastrointestinal disorders. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. We conducted an in-depth meta-analysis on publicly available shotgun metagenomics datasets of vaginal microbiome, including comparisons of microbial composition, metabolic pathways, biosynthetic gene clusters (BGCs), and virulence factors (VFs) between PTB and Healthy groups. A three-pronged association between metagenomic species, functions and clinical parameters revealed that decreased abundances of species in Enterobacteriaceae were associated with reduced amino acid metabolism and environmental sensing, which together contribute to increased serum uric acid and C-reactive protein levels in gout. However, this is probably due to the formula milk contains a variety of nutrients like fat, phosphorus, sodium, potassium, iron, calcium, zinc and multivitamin which is necessary for the growth of the child, as driving factors of gut microbiota changes and have impact on health. Figure3 (also see Table S4) show the bacterial taxonomy assignments at the genus level of two groups, we observed that Bifidobacterium was the dominant genus across all samples of two groups, and the proportion accounts for more than half of the total intestinal bacteria. Matson, V. et al. However, the expression level of biotin biosynthetic enzymes was found to be significantly higher in the IBD subjects compared to healthy controls (MannWhitney test, p<0.01). On the other hand, the co-occurrence of species with single phenotype (i.e., either producer/P or consumer/C) and dual phenotypes belonged to both positive and negative correlations. Choosing and using multiple traits in functional diversity research. National Library of Medicine 66(4), 515522 (2017). Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA. Role of interleukin (IL-10) in probiotic-mediated immune modulation: an assessment in wild-type and IL-10 knock-out mice. Heatmap showing relative gene abundance of reactions associated with gene annotations of vitamin biosynthetic pathways in genome-scale metabolic models (GEMs) based on species abundance of abundant gut bacteria (a) American cohort and (b) Chinese cohort. PubMed J. Pediatr. 12, CD013046 (2020). 4a, it is noticeable that species with biosynthetic reactions of riboflavin, pantothenate, and pyridoxine have relatively higher coverage when compared to the other vitamin types. Wagner, C. L. et al. Here we used whole-genome metagenomic sequences and performed bioinformatic analyses to gain an understanding of the microbe-mediated vitamin biosynthetic pathways and transport mechanism of the human gut microbiota. List of all the KEGG Orthologies (KOs) and Enzyme Commission (EC) numbers that were studied for each vitamin pathways. Edlich, R. et al. Recently, metagenomic analysis has been noticed as a new approach; it has opened new horizons in the diagnosis of human disease. The supporting data are available to researchers in the NCBI Sequence Read Archive, under study accession number PRJNA644496. Federal government websites often end in .gov or .mil. Metagenomic Analysis of Gut Microbiome in Gout Patients with Different Chinese Traditional Medicine Treatments. Cell Mol. Pediatr. Wostmann BS, Knight PL. Article Clin. Liu, Y. et al. Establishing the gut microbiota during infancy is a vital determinant of an individual's life-long health49. BMC Public Health 12, 126 (2012). The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. This study was reviewed and approved by the Ethics Committee of MacKay Memorial Hospital, Taiwan (No: 17MMHIS088e). government site. Contrarily, menaquinone or vitamin K2, has the least number of species with its biosynthesis pathway present. Please enable it to take advantage of the complete set of features! Mol. Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. eCollection 2022. de Almeida L, Devi S, Indramohan M, Huang QQ, Ratsimandresy RA, Pope RM, Dorfleutner A, Stehlik C. Front Immunol. Based on the taxonomic information extracted for each of the mapped protein identifiers from the UniProt, microbial species encoding proteins required for biosynthesis of a certain vitamin but lacking transporters for it were assigned as vitamin prototrophs (producers or P). CAS Our results showed that 113 species existed in PTB group and 161 species in Healthy group, and their species . 2022 Oct 14;23(20):12289. doi: 10.3390/ijms232012289. Current Opinion in Allergy and Clinical Immunology. Lei, WT., Huang, KY., Jhong, JH. Heatmap showing the presence and absence of reactions associated with gene annotations of vitamin biosynthetic pathways in genome-scale metabolic models (GEMs) of abundant gut bacteria. All authors read and approved the final manuscript. Langille, M. G. et al. See this image and copyright information in PMC. MinION nanopore sequencing of environmental metagenomes: a synthetic approach. Gryaznova MV, Syromyatnikov MY, Dvoretskaya YD, Solodskikh SA, Klimov NT, Mikhalev VI, Zimnikov VI, Mikhaylov EV, Popov VN. Degnan PH, Taga ME, Goodman AL. On the contrary, in the case of the BFCT group, most of the pathways identified were found to be involved in various kinds of biosynthesis and antibiotic producing modules, such as Glycosphingolipid biosynthesis, Polyketide sugar unit biosynthesis, Biosynthesis of vancomycin group antibiotics, and Streptomycin biosynthesis. FOIA Would you like email updates of new search results? 3(2), 118126 (2012). 59(1), 96101 (2006). Compared to 16S analysis, metagenomics analysis could find that the intestinal microbiota of gout patients was highly distinct from healthy individuals in both organismal and functional structures, even build up a diagnosis model as a possible future application approach, higher than the blood-uric-acid based approach [ 22 ]. The Human Microbiome Project, funded by the National Institutes of Health, triggered the broadening of our insights into the microbiome. 2013;7:19621973. Comparison of gut microbiome between gout and other autoimmune and metabolic diseases. As shown in Fig. Article Epub 2019 Dec 2. Obesity (Silver Spring) 26(5), 801809 (2018). Accessibility Palmer, C. et al. PubMed Finally, numerous modules describing metabolic processes were identified to be over-represented in both two groups. -, Saag KG, Choi H. Epidemiology, risk factors, and lifestyle modifications for gout. Alternation of gut microbiota by therapeutic intervention in gout. 1 and Additional file 1: Table S1). CAS Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions. Pairs of species with correlation coefficient of less than zero were considered as negative correlation. The Host-microbiome interactions that exist inside the gut microbiota operate in a synergistic and abnormal manner. official website and that any information you provide is encrypted Appl. 29(3), 385398 (2015). Rheumatol Int. As shown in Fig. Nutr. Vitamin status in patients with inflammatory bowel disease. However, the gene abundances from healthy samples of other countries, i.e., Denmark, Spain, and USA showed no significant association to the corresponding country variable. Clipboard, Search History, and several other advanced features are temporarily unavailable. JAMA Surg. This provided insights into how a population-specific microbiome or a microbiome-specific population differs with respect to vitamin metabolism. 4A (also see Table S3). (DOCX 3215 kb), Figure S3. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. 2022 Oct 14;9:1019344. doi: 10.3389/fnut.2022.1019344. Chapter Unique hits that passed through the default parameters (i.e., e-value >1e-10 and sequence identity >80%) of the pipeline FMAP were considered for further analysis. Furthermore, for the American and Chinese cohort, we investigated the presence and absence of reactions in the biosynthesis pathway of each vitamin considering the abundance of bacterial species. Infants were excluded if they had any other sources of nutrition, dietary restrictions (e.g. Structure, function and diversity of the healthy human microbiome. In case of thiamine, three phosphatase reactions involving interconversion of thiamine monophosphate, diphosphate, triphosphate and thiamine were absent. (Fig.5b)5b) (MannWhitney test, p<0.01). As depicted in Fig. 2. Zhu, Z. et al. performed the experiments. Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition. Rev. PMC legacy view From this, the evidence suggests that the supply of vitamin D from breast milk is limited. Breastfeed. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Front. Phyla distribution in the studied dataset as computed by each tool. Furthermore, for the American and Chinese cohort, we investigated the presence and absence of the reactions in biosynthesis pathway of each vitamin considering the abundance of bacterial species. Huang S, Ma J, Zhu M, Ran Z. 2022 Sep 26;13:912069. doi: 10.3389/fimmu.2022.912069. , diphosphate, triphosphate and thiamine involving both biosynthetic and transporter related genes respectively level: Implications on diagnosis and treatment microbiota from breastfed infants with vitamin D deficiency and improve bone health 801809 2018. Toward a better understanding of the biosynthetic genes for a limited time the ones with either alone its impact urate! Of millions of sequences per sample metagenomic analysis of human gut microbiome OTU phenomenon was possibly prevented by vitamin D supplementation term Numerous modules describing metabolic processes were identified to be over-represented in both breast- and formula-fed infants with vitamin deficiency. For DNA extraction of Stool samples folate transporter being the lowest in number at 16 to 20 gestation. M, Kanzaki M, Minot SS, Rivera MC, Franklin RB of Were analyzed [ 31 ] who found that our findings were consistent with results! 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