1
|
Hu X, Yu C, He Y, Zhu S, Wang S, Xu Z, You S, Jiao Y, Liu SL, Bao H. Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity. BMC Microbiol 2024; 24:119. [PMID: 38580930 PMCID: PMC10996249 DOI: 10.1186/s12866-024-03278-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity remain to be comprehensively investigated. In this study, we conducted a meta-analysis of metagenomic sequencing data from both obese and non-obese individuals across multiple cohorts, totaling 1351 fecal metagenomes. Our results demonstrate a significant decrease in both the richness and diversity of the gut bacteriome and virome in obese patients. We identified 38 bacterial species including Eubacterium sp. CAG:274, Ruminococcus gnavus, Eubacterium eligens and Akkermansia muciniphila, and 1 archaeal species, Methanobrevibacter smithii, that were significantly altered in obesity. Additionally, we observed altered abundance of five viral families: Mesyanzhinovviridae, Chaseviridae, Salasmaviridae, Drexlerviridae, and Casjensviridae. Functional analysis of the gut microbiome indicated distinct signatures associated to obesity and identified Ruminococcus gnavus as the primary driver for function enrichment in obesity, and Methanobrevibacter smithii, Akkermansia muciniphila, Ruminococcus bicirculans, and Eubacterium siraeum as functional drivers in the healthy control group. Additionally, our results suggest that antibiotic resistance genes and bacterial virulence factors may influence the development of obesity. Finally, we demonstrated that gut vOTUs achieved a diagnostic accuracy with an optimal area under the curve of 0.766 for distinguishing obesity from healthy controls. Our findings offer comprehensive and generalizable insights into the gut bacteriome and virome features associated with obesity, with the potential to guide the development of microbiome-based diagnostics.
Collapse
Affiliation(s)
- Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Songling Zhu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shuang Wang
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China.
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China.
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
| |
Collapse
|
2
|
Chanda D, De D. Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift. Gut Microbes 2024; 16:2304900. [PMID: 38265338 PMCID: PMC10810176 DOI: 10.1080/19490976.2024.2304900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
The majority of cohort-specific studies associating gut microbiota with obesity are often contradictory; thus, the replicability of the signature remains questionable. Moreover, the species that drive obesity-associated functional shifts and their replicability remain unexplored. Thus, we aimed to address these questions by analyzing gut microbial metagenome sequencing data to develop an in-depth understanding of obese host-gut microbiota interactions using 3329 samples (Obese, n = 1494; Control, n = 1835) from 17 different countries, including both 16S rRNA gene and metagenomic sequence data. Fecal metagenomic data from diverse geographical locations were curated, profiled, and pooled using a machine learning-based approach to identify robust global signatures of obesity. Furthermore, gut microbial species and pathways were systematically integrated through the genomic content of the species to identify contributors to obesity-associated functional shifts. The community structure of the obese gut microbiome was evaluated, and a reproducible depletion of diversity was observed in the obese compared to the lean gut. From this, we infer that the loss of diversity in the obese gut is responsible for perturbations in the healthy microbial functional repertoire. We identified 25 highly predictive species and 37 pathway associations as signatures of obesity, which were validated with remarkably high accuracy (AUC, Species: 0.85, and pathway: 0.80) with an independent validation dataset. We observed a reduction in short-chain fatty acid (SCFA) producers (several Alistipes species, Odoribacter splanchnicus, etc.) and depletion of promoters of gut barrier integrity (Akkermansia muciniphila and Bifidobacterium longum) in obese guts. Our analysis underlines SCFAs and purine/pyrimidine biosynthesis, carbohydrate metabolism pathways in control individuals, and amino acid, enzyme cofactor, and peptidoglycan biosynthesis pathway enrichment in obese individuals. We also mapped the contributors to important obesity-associated functional shifts and observed that these are both dataset-specific and shared across the datasets. In summary, a comprehensive analysis of diverse datasets unveils species specifically contributing to functional shifts and consistent gut microbial patterns associated to obesity.
Collapse
Affiliation(s)
- Deep Chanda
- Laboratory of Cellular Differentiation & Metabolic Disorder, Department of Biotechnology, National Institute of Technology, Durgapur, India
| | - Debojyoti De
- Laboratory of Cellular Differentiation & Metabolic Disorder, Department of Biotechnology, National Institute of Technology, Durgapur, India
| |
Collapse
|
3
|
Choi Y, Lee SJ, Kim HS, Eom JS, Jo SU, Guan LL, Seo J, Park T, Lee Y, Lee SS, Lee SS. Oral administration of Pinus koraiensis cone essential oil reduces rumen methane emission by altering the rumen microbial composition and functions in Korean native goat ( Capra hircus coreanae). Front Vet Sci 2023; 10:1168237. [PMID: 37275608 PMCID: PMC10234127 DOI: 10.3389/fvets.2023.1168237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/21/2023] [Indexed: 06/07/2023] Open
Abstract
This study aimed to investigate Pinus koraiensis cone essential oil (PEO) as a methane (CH4) inhibitor and determine its impact on the taxonomic and functional characteristics of the rumen microbiota in goats. A total of 10 growing Korean native goats (Capra hircus coreanae, 29.9 ± 1.58 kg, male) were assigned to different dietary treatments: control (CON; basal diet without additive) and PEO (basal diet +1 g/d of PEO) by a 2 × 2 crossover design. Methane measurements were conducted every 4 consecutive days for 17-20 days using a laser CH4 detector. Samples of rumen fluid and feces were collected during each experimental period to evaluate the biological effects and dry matter (DM) digestibility after PEO oral administration. The rumen microbiota was analyzed via 16S rRNA gene amplicon sequencing. The PEO oral administration resulted in reduced CH4 emission (eructation CH4/body weight0.75, p = 0.079) without affecting DM intake; however, it lowered the total volatile fatty acids (p = 0.041), molar proportion of propionate (p = 0.075), and ammonia nitrogen (p = 0.087) in the rumen. Blood metabolites (i.e., albumin, alanine transaminase/serum glutamic pyruvate transaminase, creatinine, and triglyceride) were significantly affected (p < 0.05) by PEO oral administration. The absolute fungal abundance (p = 0.009) was reduced by PEO oral administration, whereas ciliate protozoa, total bacteria, and methanogen abundance were not affected. The composition of rumen prokaryotic microbiota was altered by PEO oral administration with lower evenness (p = 0.054) observed for the PEO group than the CON group. Moreover, PICRUSt2 analysis revealed that the metabolic pathways of prokaryotic bacteria, such as pyruvate metabolism, were enriched in the PEO group. We also identified the Rikenellaceae RC9 gut group as the taxa potentially contributing to the enriched KEGG modules for histidine biosynthesis and pyruvate oxidation in the rumen of the PEO group using the FishTaco analysis. The entire co-occurrence networks showed that more nodes and edges were detected in the PEO group. Overall, these findings provide an understanding of how PEO oral administration affects CH4 emission and rumen prokaryotic microbiota composition and function. This study may help develop potential manipulation strategies to find new essential oils to mitigate enteric CH4 emissions from ruminants.
Collapse
Affiliation(s)
- Youyoung Choi
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Shin Ja Lee
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science and University-Centered Labs, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyun Sang Kim
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Jun Sik Eom
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Seong Uk Jo
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jakyeom Seo
- Department of Animal Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Yookyung Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Jeonju, Republic of Korea
| | - Sang Suk Lee
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Sunchon, Republic of Korea
| | - Sung Sill Lee
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science and University-Centered Labs, Gyeongsang National University, Jinju, Republic of Korea
| |
Collapse
|
4
|
Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, Crook DW, Read DS, Walker AS, Stoesser N. High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microb Genom 2023; 9. [PMID: 37145848 DOI: 10.1099/mgen.0.000983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
Collapse
Affiliation(s)
- Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - M Bowes
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - K Easterbrook
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - H Brett
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - J Hughes
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - D S Read
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| |
Collapse
|
5
|
Siriarchawatana P, Pumkaeo P, Harnpicharnchai P, Likhitrattanapisal S, Mayteeworakoon S, Boonsin W, Zhou X, Liang J, Cai L, Ingsriswang S. Temporal, compositional, and functional differences in the microbiome of Bangkok subway air environment. ENVIRONMENTAL RESEARCH 2023; 219:115065. [PMID: 36535389 DOI: 10.1016/j.envres.2022.115065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
With the growing numbers of the urban population, an increasing number of commuters have relied on subway systems for rapid transportation in daily life. Analyzing the temporal distribution of air microbiomes in subway environments is crucial for the assessment and monitoring of air quality in the subway system, especially with regard to public health. This study employed culture-independent metabarcode sequencing to analyze bacterial diversity and variations in bacterial compositions associated with bioaerosols collected from a subway station in Bangkok over a four-month period. The bacteria obtained were found to consist primarily of Proteobacteria, Firmicutes, and Actinobacteria, with variations at the family, genus, and species levels among samples obtained in different months. The vast majority of these bacteria are most likely derived from outside environments and human body sources. Many of the bacteria found in Bangkok subway station were also identified as "core microorganisms" of subway environments around the world, as suggested by the MetaSUB Consortium. The diversity of bacterial communities was shown to be influenced by several air quality variables, especially ambient temperature and the quantity of particulate matters, which showed positive correlations with several bacterial species such as Acinetobacter lwoffii, Staphylococcus spp., and Moraxella osloensis. In addition, metabolic profiles inferred from metabarcode-derived bacterial diversity showed significant variations across different sampling times and sites and can be used as a starting point to further explore the functional roles of specific groups of bacteria in the subway environment. This study thus introduced the information required for surveillance of microbiological impacts and their contributions to the well-being of subway commuters in Bangkok.
Collapse
Affiliation(s)
- Paopit Siriarchawatana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Panyapon Pumkaeo
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Piyanun Harnpicharnchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Somsak Likhitrattanapisal
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sermsiri Mayteeworakoon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Worawongsin Boonsin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Xin Zhou
- Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Junmin Liang
- Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Lei Cai
- Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| |
Collapse
|
6
|
Jacobs JP, Lagishetty V, Hauer MC, Labus JS, Dong TS, Toma R, Vuyisich M, Naliboff BD, Lackner JM, Gupta A, Tillisch K, Mayer EA. Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes. MICROBIOME 2023; 11:5. [PMID: 36624530 PMCID: PMC9830758 DOI: 10.1186/s40168-022-01450-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. METHODS Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers. RESULTS IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86). CONCLUSIONS IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstract.
Collapse
Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA.
| | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Megan C Hauer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer S Labus
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Tien S Dong
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Ryan Toma
- Viome Life Sciences, Bellevue, WA, USA
| | | | - Bruce D Naliboff
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeffrey M Lackner
- Division of Behavioral Medicine, Department of Medicine, Jacobs School of Medicine, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Arpana Gupta
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kirsten Tillisch
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Integrative Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Emeran A Mayer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
7
|
Douglas GM, Kim S, Langille MGI, Shapiro BJ. Efficient computation of contributional diversity metrics from microbiome data with FuncDiv. Bioinformatics 2022; 39:6909011. [PMID: 36519836 PMCID: PMC9825779 DOI: 10.1093/bioinformatics/btac809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/21/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Microbiome datasets with taxa linked to the functions (e.g. genes) they encode are becoming more common as metagenomics sequencing approaches improve. However, these data are challenging to analyze due to their complexity. Summary metrics, such as the alpha and beta diversity of taxa contributing to each function (i.e. contributional diversity), represent one approach to investigate these data, but currently there are no straightforward methods for doing so. RESULTS We addressed this gap by developing FuncDiv, which efficiently performs these computations. Contributional diversity metrics can provide novel insights that would be impossible to identify without jointly considering taxa and functions. AVAILABILITY AND IMPLEMENTATION FuncDiv is distributed under a GNU Affero General Public License v3.0 and is available at https://github.com/gavinmdouglas/FuncDiv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - Sunu Kim
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Morgan G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - B Jesse Shapiro
- Genome Centre, McGill University, Montréal, QC H3A 0G1, Canada ,Department of Microbiology & Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| |
Collapse
|
8
|
Cohen Y, Borenstein E. The microbiome's fiber degradation profile and its relationship with the host diet. BMC Biol 2022; 20:266. [PMID: 36464700 PMCID: PMC9721016 DOI: 10.1186/s12915-022-01461-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The relationship between the gut microbiome and diet has been the focus of numerous recent studies. Such studies aim to characterize the impact of diet on the composition of the microbiome, as well as the microbiome's ability to utilize various compounds in the diet and produce metabolites that may be beneficial for the host. Consumption of dietary fibers (DFs)-polysaccharides that cannot be broken down by the host's endogenous enzymes and are degraded primarily by members of the microbiome-is known to have a profound effect on the microbiome. Yet, a comprehensive characterization of microbiome compositional and functional shifts in response to the consumption of specific DFs is still lacking. RESULTS Here, we introduce a computational framework, coupling metagenomic sequencing with careful annotation of polysaccharide degrading enzymes and DF structures, for inferring the metabolic ability of a given microbiome sample to utilize a broad catalog of DFs. We demonstrate that the inferred fiber degradation profile (IFDP) generated by our framework accurately reflects the dietary habits of various hosts across four independent datasets. We further demonstrate that IFDPs are more tightly linked to the host diet than commonly used taxonomic and functional microbiome-based profiles. Finally, applying our framework to a set of ~700 metagenomes that represents large human population cohorts from 9 different countries, we highlight intriguing global patterns linking DF consumption habits with microbiome capacities. CONCLUSIONS Combined, our findings serve as a proof-of-concept for the use of DF-specific analysis for providing important complementary information for better understanding the relationship between dietary habits and the gut microbiome.
Collapse
Affiliation(s)
- Yotam Cohen
- grid.12136.370000 0004 1937 0546The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- grid.12136.370000 0004 1937 0546The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel ,grid.12136.370000 0004 1937 0546Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel ,grid.209665.e0000 0001 1941 1940Santa Fe Institute, Santa Fe, NM USA
| |
Collapse
|
9
|
Douglas GM, Hayes MG, Langille MGI, Borenstein E. Integrating phylogenetic and functional data in microbiome studies. Bioinformatics 2022; 38:5055-5063. [PMID: 36179077 PMCID: PMC9665866 DOI: 10.1093/bioinformatics/btac655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/10/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Microbiome functional data are frequently analyzed to identify associations between microbial functions (e.g. genes) and sample groups of interest. However, it is challenging to distinguish between different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed POMS, a package that implements multiple phylogeny-aware frameworks to more robustly identify enriched functions. RESULTS The key contribution is an extended balance-tree workflow that incorporates functional and taxonomic information to identify functions that are consistently enriched in sample groups across independent taxonomic lineages. Our package also includes a workflow for running phylogenetic regression. Based on simulated data we demonstrate that these approaches more accurately identify gene families that confer a selective advantage compared with commonly used tools. We also show that POMS in particular can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome. AVAILABILITY AND IMPLEMENTATION These workflows are freely available in the POMS R package at https://github.com/gavinmdouglas/POMS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Molly G Hayes
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | | |
Collapse
|
10
|
dos Santos Cruz BC, da Silva Duarte V, Sousa Dias R, Ladeira Bernardes A, de Paula SO, de Luces Fortes Ferreira CL, do Carmo Gouveia Peluzio M. Synbiotic modulates intestinal microbiota metabolic pathways and inhibits DMH-induced colon tumorigenesis through c-myc and PCNA suppression. Food Res Int 2022; 158:111379. [DOI: 10.1016/j.foodres.2022.111379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/04/2022]
|
11
|
Morgan EW, Perdew GH, Patterson AD. Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. Toxicol Sci 2022; 187:189-213. [PMID: 35285497 PMCID: PMC9154275 DOI: 10.1093/toxsci/kfac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.
Collapse
Affiliation(s)
- Ethan W Morgan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
12
|
Abstract
Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, n = 28) and healthy controls (n = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of Oscillibacter and Enterobacter was remarkably increased in patients and Blautia and Romboutsia genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND, derived from Enterobacter, were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between Enterobacter and baseline insulin-like growth factor 1 (IGF-1), indicating that Enterobacter may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. IMPORTANCE Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND were enriched in patients. Also, we were pleasantly surprised to find that the Enterobacter genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.
Collapse
|
13
|
Djemiel C, Maron PA, Terrat S, Dequiedt S, Cottin A, Ranjard L. Inferring microbiota functions from taxonomic genes: a review. Gigascience 2022; 11:giab090. [PMID: 35022702 PMCID: PMC8756179 DOI: 10.1093/gigascience/giab090] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.
Collapse
Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aurélien Cottin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| |
Collapse
|
14
|
Yanavich C, Perazzo H, Li F, Tobin N, Lee D, Zabih S, Morata M, Almeida C, Veloso VG, Grinsztejn B, Aldrovandi GM. A pilot study of microbial signatures of liver disease in those with HIV mono-infection in Rio de Janeiro, Brazil. AIDS 2022; 36:49-58. [PMID: 34873092 PMCID: PMC8667204 DOI: 10.1097/qad.0000000000003084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE The rectal microbiome was examined to assess the relationship between the microbiome and liver disease in HIV-infection. DESIGN Eighty-two HIV-1 mono-infected individuals from the PROSPEC-HIV-study (NCT02542020) were grouped into three liver health categories based on results of controlled attenuation parameter (CAP) and liver stiffness measurement (LSM) of transient elastography: normal (n = 30), steatosis (n = 30), or fibrosis (n = 22). METHODS Liver steatosis and fibrosis were defined by CAP at least 248 dB/m and LSM at least 8.0 kPa, respectively. 16S rRNA gene and whole genome shotgun metagenomic sequencing were performed on rectal swabs. Bacterial differences were assessed using zero-inflated negative binomial regression and random forests modeling; taxonomic drivers of functional shifts were identified using FishTaco. RESULTS Liver health status explained four percentage of the overall variation (r2 = 0.04, P = 0.003) in bacterial composition. Participants with steatosis had depletions of Akkermansia muciniphila and Bacteroides dorei and enrichment of Prevotella copri, Finegoldia magna, and Ruminococcus bromii. Participants with fibrosis had depletions of Bacteroides stercoris and Parabacteroides distasonis and enrichment of Sneathia sanguinegens. In steatosis, functional analysis revealed increases in primary and secondary bile acid synthesis encoded by increased Eubacterium rectale, F. magna, and Faecalibacterium prausnitzii and decreased A. muciniphila, Bacteroides fragilis and B. dorei. Decreased folate biosynthesis was driven by similar changes in microbial composition. CONCLUSION HIV mono-infection with steatosis or fibrosis had distinct microbial profiles. Some taxa are similar to those associated with non-alcoholic fatty liver disease in HIV-negative populations. Further studies are needed to define the role of the gut microbiota in the pathogenesis of liver disease in HIV-infected persons.
Collapse
Affiliation(s)
- Carolyn Yanavich
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Hugo Perazzo
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Fan Li
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Nicole Tobin
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - David Lee
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Sara Zabih
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Michelle Morata
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Cristiane Almeida
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Valdilea G Veloso
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| |
Collapse
|
15
|
Nobel YR, Rozenberg F, Park H, Freedberg DE, Blaser MJ, Green PH, Uhlemann AC, Lebwohl B. Lack of Effect of Gluten Challenge on Fecal Microbiome in Patients With Celiac Disease and Non-Celiac Gluten Sensitivity. Clin Transl Gastroenterol 2021; 12:e00441. [PMID: 34928868 PMCID: PMC8691493 DOI: 10.14309/ctg.0000000000000441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/24/2021] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Celiac disease (CD) may be associated with gut microbial dysbiosis. Whether discrete gluten exposure in subjects with well-controlled disease on a gluten-free diet impacts the gut microbiome is unknown and may have implications for understanding disease activity and symptoms. We conducted a prospective study to evaluate the impact of gluten exposure on the gut microbiome in patients with CD and nonceliac gluten sensitivity (NCGS). METHODS Subjects with CD (n = 9) and NCGS (n = 8) previously on a gluten-free diet were administered a 14-day gluten challenge (5 g of gluten per day) and compared with controls (n = 8) on a usual gluten-containing diet. Stool was collected for fecal microbiome analysis using 16S rRNA gene and metagenomic sequencing before, during, and after the gluten challenge. Symptoms were assessed using 2 validated clinical scales. RESULTS Among subjects with CD and NCGS, there were no significant fecal microbial changes in response to gluten challenge. Gut microbiome composition differed among controls, subjects with CD, and subjects with NCGS at baseline, and these differences persisted despite gluten exposure. Gastrointestinal and general health symptoms reported by subjects with CD and NCGS were worst in the middle of gluten challenge and lessened by its end, with no consistent associations with gut microbiome composition. DISCUSSION Pre-existing fecal microbiome diversity was unaffected by gluten challenge in adult subjects with CD and NCGS. These findings suggest that current microbiome status is unrelated to current disease activity and disease severity.
Collapse
Affiliation(s)
- Yael R. Nobel
- Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA;
| | - Felix Rozenberg
- Microbiome and Pathogen Genomics Collaborative Center, Columbia University Irving Medical Center, New York, New York, USA;
| | - Heekuk Park
- Microbiome and Pathogen Genomics Collaborative Center, Columbia University Irving Medical Center, New York, New York, USA;
| | - Daniel E. Freedberg
- Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA;
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, USA;
| | - Peter H.R. Green
- Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA;
- Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA;
| | - Anne-Catrin Uhlemann
- Microbiome and Pathogen Genomics Collaborative Center, Columbia University Irving Medical Center, New York, New York, USA;
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA.
| | - Benjamin Lebwohl
- Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA;
- Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA;
| |
Collapse
|
16
|
Tong X, Leung MHY, Shen Z, Lee JYY, Mason CE, Lee PKH. Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. MICROBIOME 2021; 9:213. [PMID: 34724986 PMCID: PMC8562002 DOI: 10.1186/s40168-021-01166-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail. RESULTS Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography. CONCLUSIONS Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures. Video Abstract.
Collapse
Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
17
|
Eng A, Hayden HS, Pope CE, Brittnacher MJ, Vo AT, Weiss EJ, Hager KR, Leung DH, Heltshe SL, Raftery D, Miller SI, Hoffman LR, Borenstein E. Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences. BMC Microbiol 2021; 21:247. [PMID: 34525965 PMCID: PMC8444586 DOI: 10.1186/s12866-021-02305-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Background Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth. Recent evidence identified altered fecal microbiota taxonomic compositions in infants with CF relative to healthy infants that were characterized by differences in the abundances of taxa associated with GI health and nutrition. Furthermore, these taxonomic differences were more pronounced in low length infants with CF, suggesting a potential link to linear growth failure. We hypothesized that these differences would entail shifts in the microbiome’s functional capacities that could contribute to inflammation and nutritional failure in infants with CF. Results To test this hypothesis, we compared fecal microbial metagenomic content between healthy infants and infants with CF, supplemented with an analysis of fecal metabolomes in infants with CF. We identified notable differences in CF fecal microbial functional capacities, including metabolic and environmental response functions, compared to healthy infants that intensified during the first year of life. A machine learning-based longitudinal metagenomic age analysis of healthy and CF fecal metagenomic functional profiles further demonstrated that these differences are characterized by a CF-associated delay in the development of these functional capacities. Moreover, we found metagenomic differences in functions related to metabolism among infants with CF that were associated with diet and antibiotic exposure, and identified several taxa as potential drivers of these functional differences. An integrated metagenomic and metabolomic analysis further revealed that abundances of several fecal GI metabolites important for nutrient absorption, including three bile acids, correlated with specific microbes in infants with CF. Conclusions Our results highlight several metagenomic and metabolomic factors, including bile acids and other microbial metabolites, that may impact nutrition, growth, and GI health in infants with CF. These factors could serve as promising avenues for novel microbiome-based therapeutics to improve health outcomes in these infants. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02305-z.
Collapse
Affiliation(s)
- Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | | | - Anh T Vo
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Eli J Weiss
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle R Hager
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Samuel I Miller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Pediatrics, University of Washington, Seattle, WA, USA. .,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA, USA.
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Santa Fe Institute, Santa Fe, NM, USA.
| |
Collapse
|
18
|
Joyce H, Taylor MR, Moffat A, Hong M, Isaac D, Fine N, Greenway SC. Changes in the Composition and Function of the Human Salivary Microbiome After Heart Transplantation: A Pilot Study. TRANSPLANT RESEARCH AND RISK MANAGEMENT 2021. [DOI: 10.2147/trrm.s328467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
19
|
Gomez MV, Dutta M, Suvorov A, Shi X, Gu H, Mani S, Yue Cui J. Early Life Exposure to Environmental Contaminants (BDE-47, TBBPA, and BPS) Produced Persistent Alterations in Fecal Microbiome in Adult Male Mice. Toxicol Sci 2021; 179:14-30. [PMID: 33078840 DOI: 10.1093/toxsci/kfaa161] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is a pivotal player in toxicological responses. We investigated the effects of maternal exposure to 3 human health-relevant toxicants (BDE-47, tetrabromobisphenol [TBBPA], and bisphenol S [BPS]) on the composition and metabolite levels (bile acids [BAs] and short-chain fatty acids [SCFAs]) of the gut microbiome in adult pups. CD-1 mouse dams were orally exposed to vehicle (corn oil, 10 ml/kg), BDE-47 (0.2 mg/kg), TBBPA (0.2 mg/kg), or BPS (0.2 mg/kg) once daily from gestational day 8 to the end of lactation (postnatal day 21). 16S rRNA sequencing and targeted metabolomics were performed in feces of 20-week-old adult male pups (n = 14 - 23/group). Host gene expression and BA levels were quantified in liver. BPS had the most prominent effect on the beta-diversity of the fecal microbiome compared with TBPPA and BDE-47 (QIIME). Seventy-three taxa were persistently altered by at least 1 chemical, and 12 taxa were commonly regulated by all chemicals (most of which were from the Clostridia class and were decreased). The most distinct microbial biomarkers were S24-7 for BDE-47, Rikenellaceae for TBBPA, and Lactobacillus for BPS (LefSe). The community-wide contributions to the shift in microbial pathways were predicted using FishTaco. Consistent with FishTaco predictions, BDE-47 persistently increased fecal and hepatic BAs within the 12α hydroxylation pathway, corresponding to an up-regulation with the hepatic BA-synthetic enzyme Cyp7a1. Fecal BAs were also persistently up-regulated by TBBPA and BPS (liquid chromatography-mass spectrometry). TBBPA increased propionic acid and succinate, whereas BPS decreased acetic acid (gas chromatography-mass spectrometry). There was a general trend in the hepatic down-regulation of proinflammatory cytokines and the oxidative stress sensor target gene (Nqo1), and a decrease in G6Pdx (the deficiency of which leads to dyslipidemia). In conclusion, maternal exposure to these toxicants persistently modified the gut-liver axis, which may produce an immune-suppressive and dyslipidemia-prone signature later in life.
Collapse
Affiliation(s)
- Matthew V Gomez
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Moumita Dutta
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Alexander Suvorov
- Environmental Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Xiaojian Shi
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Sridhar Mani
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| |
Collapse
|
20
|
Leung MHY, Tong X, Bøifot KO, Bezdan D, Butler DJ, Danko DC, Gohli J, Green DC, Hernandez MT, Kelly FJ, Levy S, Mason-Buck G, Nieto-Caballero M, Syndercombe-Court D, Udekwu K, Young BG, Mason CE, Dybwad M, Lee PKH. Characterization of the public transit air microbiome and resistome reveals geographical specificity. MICROBIOME 2021; 9:112. [PMID: 34039416 PMCID: PMC8157753 DOI: 10.1186/s40168-021-01044-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. RESULTS City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. CONCLUSIONS Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.
Collapse
Affiliation(s)
- M H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - X Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - K O Bøifot
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - D Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D C Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - J Gohli
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - D C Green
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M T Hernandez
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - F J Kelly
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - S Levy
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - G Mason-Buck
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M Nieto-Caballero
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - D Syndercombe-Court
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - K Udekwu
- Department of Aquatic Sciences & Assessment, Swedish University of Agriculture, Uppsala, Sweden
| | - B G Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - M Dybwad
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway.
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK.
| | - P K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
21
|
Nguyen TT, Kosciolek T, Daly RE, Vázquez-Baeza Y, Swafford A, Knight R, Jeste DV. Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk. Brain Behav Immun 2021; 91:245-256. [PMID: 33098964 PMCID: PMC8023565 DOI: 10.1016/j.bbi.2020.10.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
Emerging evidence has linked the gut microbiome changes to schizophrenia. However, there has been limited research into the functional pathways by which the gut microbiota contributes to the phenotype of persons with chronic schizophrenia. We characterized the composition and functional potential of the gut microbiota in 48 individuals with chronic schizophrenia and 48 matched (sequencing plate, age, sex, BMI, and antibiotic use) non-psychiatric comparison subjects (NCs) using 16S rRNA sequencing. Patients with schizophrenia demonstrated significant beta-diversity differences in microbial composition and predicted genetic functional potential compared to NCs. Alpha-diversity of taxa and functional pathways were not different between groups. Random forests analyses revealed that the microbiome predicts differentiation of patients with schizophrenia from NCs using taxa (75% accuracy) and functional profiles (67% accuracy for KEGG orthologs, 70% for MetaCyc pathways). We utilized a new compositionally-aware method incorporating reference frames to identify differentially abundant microbes and pathways, which revealed that Lachnospiraceae is associated with schizophrenia. Functional pathways related to trimethylamine-N-oxide reductase and Kdo2-lipid A biosynthesis were altered in schizophrenia. These metabolic pathways were associated with inflammatory cytokines and risk for coronary heart disease in schizophrenia. Findings suggest potential mechanisms by which the microbiota may impact the pathophysiology of the disease through modulation of functional pathways related to immune signaling/response and lipid and glucose regulation to be further investigated in future studies.
Collapse
Affiliation(s)
- Tanya T Nguyen
- Department of Psychiatry, University of California, San Diego, CA, United States; Sam and Rose Stein Institute for Research on Aging, University of California, San Diego, CA, United States.
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California, San Diego, CA, United States; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rebecca E Daly
- Sam and Rose Stein Institute for Research on Aging, University of California, San Diego, CA, United States
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, University of California, San Diego, CA, United States
| | - Austin Swafford
- Center for Microbiome Innovation, University of California, San Diego, CA, United States
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA, United States; Center for Microbiome Innovation, University of California, San Diego, CA, United States; Department of Computer Science and Engineering, University of California, San Diego, CA, United States; Department of Computer Science and Engineering, University of California, San Diego, CA, United States
| | - Dilip V Jeste
- Department of Psychiatry, University of California, San Diego, CA, United States; Department of Pediatrics, University of California, San Diego, CA, United States; Center for Microbiome Innovation, University of California, San Diego, CA, United States; Department of Neurosciences, University of California, San Diego, CA, United States
| |
Collapse
|
22
|
Park SY, Ufondu A, Lee K, Jayaraman A. Emerging computational tools and models for studying gut microbiota composition and function. Curr Opin Biotechnol 2020; 66:301-311. [PMID: 33248408 PMCID: PMC7744364 DOI: 10.1016/j.copbio.2020.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
Abstract
The gut microbiota and its metabolites play critical roles in human health and disease. Advances in high-throughput sequencing, mass spectrometry, and other omics assay platforms have improved our ability to generate large volumes of data exploring the temporal variations in the compositions and functions of microbial communities. To elucidate mechanisms, methods and tools are needed that can rigorously model the dependencies within time-series data. Longitudinal data are often sparse and unevenly sampled, and nontrivial challenges remain in determining statistical significance, normalization across different data types, and model validation. In this review, we highlight recent developments in models and software tools for the analysis of time series microbiome and metabolome data, as well as integration of these data.
Collapse
Affiliation(s)
- Seo-Young Park
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA
| | - Arinzechukwu Ufondu
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA.
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA; Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
23
|
Bar N, Korem T, Weissbrod O, Zeevi D, Rothschild D, Leviatan S, Kosower N, Lotan-Pompan M, Weinberger A, Le Roy CI, Menni C, Visconti A, Falchi M, Spector TD, Adamski J, Franks PW, Pedersen O, Segal E. A reference map of potential determinants for the human serum metabolome. Nature 2020; 588:135-140. [DOI: 10.1038/s41586-020-2896-2] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
|
24
|
Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.
Collapse
Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
| |
Collapse
|
25
|
Goldberg MR, Mor H, Magid Neriya D, Magzal F, Muller E, Appel MY, Nachshon L, Borenstein E, Tamir S, Louzoun Y, Youngster I, Elizur A, Koren O. Microbial signature in IgE-mediated food allergies. Genome Med 2020; 12:92. [PMID: 33109272 PMCID: PMC7592384 DOI: 10.1186/s13073-020-00789-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/06/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Multiple studies suggest a key role for gut microbiota in IgE-mediated food allergy (FA) development, but to date, none has studied it in the persistent state. METHODS To characterize the gut microbiota composition and short-chain fatty acid (SCFAs) profiles associated with major food allergy groups, we recruited 233 patients with FA including milk (N = 66), sesame (N = 38), peanut (N = 71), and tree nuts (N = 58), and non-allergic controls (N = 58). DNA was isolated from fecal samples, and 16S rRNA gene sequences were analyzed. SCFAs in stool were analyzed from patients with a single allergy (N = 84) and controls (N = 31). RESULTS The gut microbiota composition of allergic patients was significantly different compared to age-matched controls both in α-diversity and β-diversity. Distinct microbial signatures were noted for FA to different foods. Prevotella copri (P. copri) was the most overrepresented species in non-allergic controls. SCFAs levels were significantly higher in the non-allergic compared to the FA groups, whereas P. copri significantly correlated with all three SCFAs. We used these microbial differences to distinguish between FA patients and non-allergic healthy controls with an area under the curve of 0.90, and for the classification of FA patients according to their FA types using a supervised learning algorithm. Bacteroides and P. copri were identified as taxa potentially contributing to KEGG acetate-related pathways enriched in non-allergic compared to FA. In addition, overall pathway dissimilarities were found among different FAs. CONCLUSIONS Our results demonstrate a link between IgE-mediated FA and the composition and metabolic activity of the gut microbiota.
Collapse
Affiliation(s)
- Michael R Goldberg
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
- Department of Pediatrics, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Hadar Mor
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Dafna Magid Neriya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Faiga Magzal
- MIGAL-Galilee Research Institute, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
| | - Efrat Muller
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Michael Y Appel
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
| | - Liat Nachshon
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
- Department of Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, NM, USA
| | - Snait Tamir
- MIGAL-Galilee Research Institute, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat-Gan, Israel
| | - Ilan Youngster
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
- Department of Pediatrics, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Arnon Elizur
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
- Department of Pediatrics, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
| |
Collapse
|
26
|
Uzan-Yulzari A, Morr M, Tareef-Nabwani H, Ziv O, Magid-Neriya D, Armoni R, Muller E, Leibovici A, Borenstein E, Louzoun Y, Shai A, Koren O. The intestinal microbiome, weight, and metabolic changes in women treated by adjuvant chemotherapy for breast and gynecological malignancies. BMC Med 2020; 18:281. [PMID: 33081767 PMCID: PMC7576808 DOI: 10.1186/s12916-020-01751-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Adjuvant chemotherapy induces weight gain, glucose intolerance, and hypertension in about a third of women. The mechanisms underlying these events have not been defined. This study assessed the association between the microbiome and weight gain in patients treated with adjuvant chemotherapy for breast and gynecological cancers. METHODS Patients were recruited before starting adjuvant therapy. Weight and height were measured before treatment and 4-6 weeks after treatment completion. Weight gain was defined as an increase of 3% or more in body weight. A stool sample was collected before treatment, and 16S rRNA gene sequencing was performed. Data regarding oncological therapy, menopausal status, and antibiotic use was prospectively collected. Patients were excluded if they were treated by antibiotics during the study. Fecal transplant experiments from patients were conducted using Swiss Webster germ-free mice. RESULTS Thirty-three patients were recruited; of them, 9 gained 3.5-10.6% of baseline weight. The pretreatment microbiome of women who gained weight following treatment was significantly different in diversity and taxonomy from that of control women. Fecal microbiota transplantation from pretreatment samples of patients that gained weight induced metabolic changes in germ-free mice compared to mice transplanted with pretreatment fecal samples from the control women. CONCLUSION The microbiome composition is predictive of weight gain following adjuvant chemotherapy and induces adverse metabolic changes in germ-free mice, suggesting it contributes to adverse metabolic changes seen in patients. Confirmation of these results in a larger patient cohort is warranted.
Collapse
Affiliation(s)
| | - Maya Morr
- Department of Oncology, Galilee Medical Center, Nahariya, Israel
| | | | - Oren Ziv
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Ran Armoni
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Efrat Muller
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Anca Leibovici
- Department of Oncology, Galilee Medical Center, Nahariya, Israel
| | - Elhanan Borenstein
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Santa Fe Institute, Santa Fe, NM, USA
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Ayelet Shai
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Department of Oncology, Galilee Medical Center, Nahariya, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
| |
Collapse
|
27
|
Abstract
The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis. The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses.
Collapse
|
28
|
Xu D, Wang N, Rinne M, Ke W, Weinberg ZG, Da M, Bai J, Zhang Y, Li F, Guo X. The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants. Microb Biotechnol 2020; 14:561-576. [PMID: 32627363 PMCID: PMC7936295 DOI: 10.1111/1751-7915.13623] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/11/2020] [Accepted: 06/11/2020] [Indexed: 01/14/2023] Open
Abstract
Multi‐omics approach was adopted to investigate the modulation of bacterial microbiota and metabolome as well as their interactions in whole crop corn ensiling systems by inoculating homofermentative Lactobacillus plantarum or heterofermentative Lactobacillus buchneri. Inoculations of the two different inoculants resulted in substantial differences in microbial community and metabolic composition as well as their dynamics in ensiled corn. Inoculants also altered the correlations of microbiota in different manners, and various keystone species were identified in corn silages with different treatments. Many metabolites with biofunctional activities like bacteriostatic, antioxidant, central nervous system inhibitory and anti‐inflammatory were found in the present silage. A constitutive difference in microbiota dynamics was found for several pathways, which were upregulated by specific taxa in middle stage of fermentation, and widespread associations between metabolites with biofunctions and the species of lactic acid bacteria dominated in silage were observed. Multiple microbial and metabolic structures and dynamics were correlated and affected the fermentation process of the corn ensiling systems. Results of the current study improve our understanding of the complicated biological process underlying silage fermentation and provide a framework to re‐evaluate silages with biofunctions, which may contribute to target‐based regulation methods to produce functional silage for animal production.
Collapse
Affiliation(s)
- Dongmei Xu
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Nian Wang
- Nextomics Biosciences Institute, Wuhan, 430000, China
| | - Marketta Rinne
- Natural Resources Institute Finland (Luke) Animale, Jokioinen, 31600, Finland
| | - Wencan Ke
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Zwika G Weinberg
- Microbial Food-Safety Research Unit, Department of Food Quality and Safety, The Volcani Center, Agriculture Research Organization, Institute for Postharvest and Food Sciences, Derech HaMaccabim Road 68, POB 15159, Rishon-LeZion, 7528809, Israel
| | - Mi Da
- Nextomics Biosciences Institute, Wuhan, 430000, China
| | - Jie Bai
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Yixin Zhang
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Fuhou Li
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Xusheng Guo
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| |
Collapse
|
29
|
Park T, Ma L, Ma Y, Zhou X, Bu D, Yu Z. Dietary energy sources and levels shift the multi-kingdom microbiota and functions in the rumen of lactating dairy cows. J Anim Sci Biotechnol 2020; 11:66. [PMID: 32582444 PMCID: PMC7310258 DOI: 10.1186/s40104-020-00461-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/13/2020] [Indexed: 11/23/2022] Open
Abstract
Background Dietary energy source and level in lactation diets can profoundly affect milk yield and composition. Such dietary effects on lactation performance are underpinned by alteration of the rumen microbiota, of which bacteria, archaea, fungi, and protozoa may vary differently. However, few studies have examined all the four groups of rumen microbes. This study investigated the effect of both the level and source of dietary energy on rumen bacteria, archaea, fungi, and protozoa in the rumen of lactating dairy cows. A 2 × 2 factorial design resulted in four dietary treatments: low and high dietary energy levels (LE: 1.52–1.53; and HE: 1.71–1.72 Mcal/kg dry matter) and two dietary energy sources (GC: finely ground corn; and SFC: steam-flaked corn). We used a replicated 4 × 4 Latin square design using eight primiparous Chinese Holstein cows with each period lasting for 21 d. The rumen microbiota was analyzed using metataxonomics based on kingdom-specific phylogenetic markers [16S rRNA gene for bacteria and archaea, 18S rRNA gene for protozoa, and internally transcribed spacer 1 (ITS1) for fungi] followed with subsequent functional prediction using PICRUSt2. Results The GC resulted in a higher prokaryotic (bacterial and archaeal) species richness and Faith’s phylogenetic diversity than SFC. For the eukaryotic (fungi and protozoa) microbiota, the LE diets led to significantly higher values of the above measurements than the HE diets. Among the major classified taxa, 23 genera across all the kingdoms differed in relative abundance between the two dietary energy levels, while only six genera (none being protozoal) were differentially abundant between the two energy sources. Based on prokaryotic amplicon sequence variants (ASVs) from all the samples, overall functional profiles predicted using PICRUSt2 differed significantly between LE and HE but not between the two energy sources. FishTaco analysis identified Ruminococcus and Coprococcus as the taxa potentially contributing to the enriched KEGG pathways for biosynthesis of amino acids and to the metabolisms of pyruvate, glycerophospholipid, and nicotinate and nicotinamide in the rumen of HE-fed cows. The co-occurrence networks were also affected by the dietary treatments, especially the LE and GC diets, resulting in distinct co-occurrence networks. Several microbial genera appeared to be strongly correlated with one or more lactation traits. Conclusions Dietary energy level affected the overall rumen multi-kingdom microbiota while little difference was noted between ground corn and steam-flaked corn. Some genera were also affected differently by the four dietary treatments, including genera that had been shown to be correlated with lactation performance or feed efficiency. The co-occurrence patterns among the genera exclusively found for each dietary treatment may suggest possible metabolic interactions specifically affected by the dietary treatment. Some of the major taxa were positively correlated to milk properties and may potentially serve as biomarkers of one or more lactation traits.
Collapse
Affiliation(s)
- Tansol Park
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
| | - Lu Ma
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ying Ma
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaoqiao Zhou
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Dengpan Bu
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.,CAAS-ICRAF Joint Lab on Agroforestry and Sustainable Animal Husbandry, Beijing, P. R. China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
| |
Collapse
|
30
|
Kim M, Park T, Jeong JY, Baek Y, Lee HJ. Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle. Animals (Basel) 2020; 10:ani10040712. [PMID: 32325868 PMCID: PMC7222830 DOI: 10.3390/ani10040712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/04/2020] [Accepted: 04/16/2020] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The ruminal microbiome affects various metabolic processes associated with animal development; however, few studies have focused on its correlation with marbling. Results of the present study show differences in ruminal microbiomes among Hanwoo Korean beef cattle, which have low or high marbling scores. By elucidating the effect of the ruminal microbiome on the marbling of Hanwoo, differentially abundant microbial taxa, ruminal taxonomic drivers of lipid metabolism, and the correlation with meat quality indices, the present study provides insights into the potential effects of microbial factors on marbling in beef cattle. Abstract This study demonstrated the potential effects of the rumen microbiota on the deposition of intramuscular fat, known as marbling. Previous studies on fatty acid metabolism in beef cattle have mostly focused on biohydrogenating rumen bacteria, whereas those on the overall rumen microbiota—to understand their roles in marbling—have not been systematically performed. The rumen microbiota of 14 Korean beef cattle (Hanwoo), which showed similar carcass characteristics and blood metabolites but different marbling scores, were analyzed by 16S rRNA gene sequencing. The rumen samples were grouped into two extreme marbling score groups of host animals as follows: LMS, marbling score≤ 4 or HMS, marbling score ≥7. Species richness tended to be higher in the HMS group, whereas the overall microbiota differed between LMS and HMS groups. RFP12, Verrucomicrobia, Oscillospira, Porphyromonadaceae, and Paludibacter were differentially abundant in the HMS group, whereas Olsenella was abundant in the LMS group. Some marbling-associated bacterial taxa also contributed to the enrichment of two lipid metabolic pathways including “alpha-linolenic acid metabolism” and “fatty acid biosynthesis” in the HMS microbiome. Taxonomic drivers of fatty acid biosynthesis, particularly in the rumen microbiome of high-marbled meat, could thus be further studied to increase the intramuscular fat content.
Collapse
Affiliation(s)
- Minseok Kim
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea; (M.K.); (J.Y.J.); (Y.B.)
- Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Tansol Park
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA;
| | - Jin Young Jeong
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea; (M.K.); (J.Y.J.); (Y.B.)
| | - Youlchang Baek
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea; (M.K.); (J.Y.J.); (Y.B.)
| | - Hyun-Jeong Lee
- Dairy Science Division, National Institute of Animal Science, Cheonan 31000, Korea
- Correspondence: ; Tel.: +82-41-580-3419
| |
Collapse
|
31
|
Abdelsalam NA, Ramadan AT, ElRakaiby MT, Aziz RK. Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics. Front Pharmacol 2020; 11:390. [PMID: 32372951 PMCID: PMC7179069 DOI: 10.3389/fphar.2020.00390] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.
Collapse
Affiliation(s)
| | - Ahmed Tarek Ramadan
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Marwa Tarek ElRakaiby
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy Karam Aziz
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| |
Collapse
|
32
|
Dovrolis N, Kolios G, Spyrou GM, Maroulakou I. Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders. Brief Bioinform 2020; 20:825-841. [PMID: 29186317 DOI: 10.1093/bib/bbx154] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/17/2017] [Indexed: 12/14/2022] Open
Abstract
Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.
Collapse
|
33
|
Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
Collapse
Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
| |
Collapse
|
34
|
Norouzi-Beirami MH, Marashi SA, Banaei-Moghaddam AM, Kavousi K. Beyond Taxonomic Analysis of Microbiomes: A Functional Approach for Revisiting Microbiome Changes in Colorectal Cancer. Front Microbiol 2020; 10:3117. [PMID: 32038558 PMCID: PMC6990412 DOI: 10.3389/fmicb.2019.03117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 12/24/2019] [Indexed: 01/16/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers in the world, especially in developed countries. In different studies, the association between CRC and dysbiosis of gut microbiome has been reported. However, most of these works focus on the taxonomic variation of the microbiome, which presents little, if any, functional insight about the reason behind and/or consequences of microbiome dysbiosis. In this study, we used a previously reported metagenome dataset which is obtained by sequencing 156 microbiome samples of healthy individuals as the control group (Co), as well as microbiome samples of patients with advanced colorectal adenoma (Ad) and colorectal carcinoma (Ca). Features of the microbiome samples have been analyzed at the level of species, as well as four functional levels, i.e., gene, KEGG orthology (KO) group, Enzyme Commission (EC) number, and reaction. It was shown that, at each of these levels, certain features exist which show significant changing trends during cancer progression. In the next step, a list of these features were extracted, which were shown to be able to predict the category of Co, Ad, and Ca samples with an accuracy of >85%. When only one group of features (species, gene, KO group, EC number, reaction) was used, KO-related features were found to be the most successful features for classifying the three categories of samples. Notably, species-related features showed the least success in sample classification. Furthermore, by applying an independent test set, we showed that these performance trends are not limited to our original dataset. We determined the most important classification features at each of the four functional levels. We propose that these features can be considered as biomarkers of CRC progression. Finally, we show that the intra-diversity of each sample at the levels of bacterial species and genes is much more than those of the KO groups, EC numbers, and reactions of that sample. Therefore, we conclude that the microbiome diversity at the species level, or gene level, is not necessarily associated with the diversity at the functional level, which again indicates the importance of KO-, EC-, and reaction-based features in metagenome analysis. The source code of proposed method is freely available from https://www.bioinformatics.org/mamed.
Collapse
Affiliation(s)
- Mohammad Hossein Norouzi-Beirami
- Laboratory of Complex Biological Systems and Bioinformatics, Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sayed-Amir Marashi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics, Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics, Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| |
Collapse
|
35
|
Rawi MH, Zaman SA, Pa'ee KF, Leong SS, Sarbini SR. Prebiotics metabolism by gut-isolated probiotics. Journal of Food Science and Technology 2020; 57:2786-2799. [PMID: 32624588 DOI: 10.1007/s13197-020-04244-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/22/2019] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
There are numerous species of bacteria resides in the lumen of human colon. The word 'colon', resembles colony or the colonization of microbiota of which plays an important role in the fermentation of prebiotics. The standpoint of prebiotic nowadays is well reported for attenuating gut dysbiosis in many clinical studies tested on animals and human. However, because of the huge amount of gut microbiome, the attempt to connect the dots between bacterial population and the host are not plainly discernible. Thus, a need to analyse recent research on the pathways of prebiotic metabolism adopted by commonly studied probiotics i.e. Bifidobacteria and Lactobacillus. Several different substrate-dependent gene expressions are induced to break down oligosaccharide molecules shown by those probiotics. The hydrolysis can occur either by membrane bound (extracellular) or cytoplasmic (intracellular) enzyme of the enteric bacteria. Therefore, this review narrates several prebiotic metabolisms occur during gut fermentation, and metabolite production i.e. organic acids conversion.
Collapse
Affiliation(s)
- Muhamad Hanif Rawi
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| | - Siti Aisyah Zaman
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| | - Khairul Faizal Pa'ee
- Food Technology Section, Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and Bio-Engineering Technology (UniKL-MICET), Bandar Vendor, Taboh Naning, 78000 Alor Gajah, Melaka Malaysia
| | - Sui Sien Leong
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| | - Shahrul Razid Sarbini
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| |
Collapse
|
36
|
Affiliation(s)
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | | | - Sasha G. Tetu
- Department of Molecular Sciences Macquarie University North Ryde NSW Australia
| | - Michael R. Gillings
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
| |
Collapse
|
37
|
Abstract
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
Collapse
|
38
|
Noecker C, Chiu HC, McNally CP, Borenstein E. Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies. mSystems 2019; 4:e00579-19. [PMID: 31848305 PMCID: PMC6918031 DOI: 10.1128/msystems.00579-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/20/2019] [Indexed: 01/24/2023] Open
Abstract
Correlation-based analysis of paired microbiome-metabolome data sets is becoming a widespread research approach, aiming to comprehensively identify microbial drivers of metabolic variation. To date, however, the limitations of this approach and other microbiome-metabolome analysis methods have not been comprehensively evaluated. To address this challenge, we have introduced a mathematical framework to quantify the contribution of each taxon to metabolite variation based on uptake and secretion fluxes. We additionally used a multispecies metabolic model to simulate simplified gut communities, generating idealized microbiome-metabolome data sets. We then compared observed taxon-metabolite correlations in these data sets to calculated ground truth taxonomic contribution values. We found that in simulations of both a representative simple 10-species community and complex human gut microbiota, correlation-based analysis poorly identified key contributors, with an extremely low predictive value despite the idealized setting. We further demonstrate that the predictive value of correlation analysis is strongly influenced by both metabolite and taxon properties, as well as by exogenous environmental variation. We finally discuss the practical implications of our findings for interpreting microbiome-metabolome studies.IMPORTANCE Identifying the key microbial taxa responsible for metabolic differences between microbiomes is an important step toward understanding and manipulating microbiome metabolism. To achieve this goal, researchers commonly conduct microbiome-metabolome association studies, comprehensively measuring both the composition of species and the concentration of metabolites across a set of microbial community samples and then testing for correlations between microbes and metabolites. Here, we evaluated the utility of this general approach by first developing a rigorous mathematical definition of the contribution of each microbial taxon to metabolite variation and then examining these contributions in simulated data sets of microbial community metabolism. We found that standard correlation-based analysis of our simulated microbiome-metabolome data sets can identify true contributions with very low predictive value and that its performance depends strongly on specific properties of both metabolites and microbes, as well as on those of the surrounding environment. Combined, our findings can guide future interpretation and validation of microbiome-metabolome studies.
Collapse
Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hsuan-Chao Chiu
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, New Mexico, USA
| |
Collapse
|
39
|
Bender JM, Li F, Purswani H, Capretz T, Cerini C, Zabih S, Hung L, Francis N, Chin S, Pannaraj PS, Aldrovandi G. Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome. J Matern Fetal Neonatal Med 2019; 34:3335-3343. [PMID: 31744351 DOI: 10.1080/14767058.2019.1684466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time. MATERIALS AND METHODS Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed. RESULTS A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R2 = 0.044, p = .002) but later courses did not (R2 = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome. CONCLUSION Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.
Collapse
Affiliation(s)
- Jeffrey M Bender
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Fan Li
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Heena Purswani
- Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Taylor Capretz
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Chiara Cerini
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Sara Zabih
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Long Hung
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nicole Francis
- Department of Pediatrics, Kaiser Permanente, Southern California Permanente Medical Group, Los Angeles, California, USA
| | - Steven Chin
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Pia S Pannaraj
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Grace Aldrovandi
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
40
|
Lv X, Chai J, Diao Q, Huang W, Zhuang Y, Zhang N. The Signature Microbiota Drive Rumen Function Shifts in Goat Kids Introduced to Solid Diet Regimes. Microorganisms 2019; 7:microorganisms7110516. [PMID: 31683646 PMCID: PMC6921049 DOI: 10.3390/microorganisms7110516] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 11/24/2022] Open
Abstract
The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production.
Collapse
Affiliation(s)
- Xiaokang Lv
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Jianmin Chai
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Qiyu Diao
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Wenqin Huang
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Yimin Zhuang
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Naifeng Zhang
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| |
Collapse
|
41
|
Dempsey JL, Little M, Cui JY. Gut microbiome: An intermediary to neurotoxicity. Neurotoxicology 2019; 75:41-69. [PMID: 31454513 DOI: 10.1016/j.neuro.2019.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/04/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
There is growing recognition that the gut microbiome is an important regulator for neurological functions. This review provides a summary on the role of gut microbiota in various neurological disorders including neurotoxicity induced by environmental stressors such as drugs, environmental contaminants, and dietary factors. We propose that the gut microbiome remotely senses and regulates CNS signaling through the following mechanisms: 1) intestinal bacteria-mediated biotransformation of neurotoxicants that alters the neuro-reactivity of the parent compounds; 2) altered production of neuro-reactive microbial metabolites following exposure to certain environmental stressors; 3) bi-directional communication within the gut-brain axis to alter the intestinal barrier integrity; and 4) regulation of mucosal immune function. Distinct microbial metabolites may enter systemic circulation and epigenetically reprogram the expression of host genes in the CNS, regulating neuroinflammation, cell survival, or cell death. We will also review the current tools for the study of the gut-brain axis and provide some suggestions to move this field forward in the future.
Collapse
Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, United States
| | - Mallory Little
- Department of Environmental and Occupational Health Sciences, University of Washington, United States
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, United States.
| |
Collapse
|
42
|
Chen J, McIlroy SE, Archana A, Baker DM, Panagiotou G. A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. MICROBIOME 2019; 7:104. [PMID: 31307536 PMCID: PMC6632204 DOI: 10.1186/s40168-019-0714-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/17/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere. RESULTS Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants. CONCLUSIONS Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.
Collapse
Affiliation(s)
- Jiarui Chen
- Systems Biology & Bioinformatics Group, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
| | - Shelby E McIlroy
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong SAR, China
| | - Anand Archana
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China
| | - David M Baker
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong SAR, China.
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China.
| | - Gianni Panagiotou
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoll Institute, Beutenbergstrasse 11a, Jena, 07745, Germany.
- Department of Microbiology Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Systems Biology & Bioinformatics Group, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
43
|
Velsko IM, Fellows Yates JA, Aron F, Hagan RW, Frantz LAF, Loe L, Martinez JBR, Chaves E, Gosden C, Larson G, Warinner C. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. MICROBIOME 2019; 7:102. [PMID: 31279340 PMCID: PMC6612086 DOI: 10.1186/s40168-019-0717-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/24/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates. RESULTS Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins. CONCLUSIONS Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.
Collapse
Affiliation(s)
- Irina M Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Richard W Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, OX2 0ES, UK
| | | | - Eros Chaves
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA
- Current address: Pinellas Dental Specialties, Largo, FL, 33776, USA
| | - Chris Gosden
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
| |
Collapse
|
44
|
Dahlin M, Prast-Nielsen S. The gut microbiome and epilepsy. EBioMedicine 2019; 44:741-746. [PMID: 31160269 PMCID: PMC6604367 DOI: 10.1016/j.ebiom.2019.05.024] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Recently, evidence from both animal studies and human cases has emerged that a dysbiosis in the gut may be associated with certain forms of epilepsy. The ketogenic diet is an alternative treatment of drug-resistant epilepsy, although its precise mechanism of action has been unclear. It has now been shown that the ketogenic diet changes the composition and function of the gut microbiome in epilepsy patients. Studies in mice have demonstrated that the gut microbiota was necessary for the therapeutic effect of the diet and a mechanism of action has been proposed, providing new potential strategies for treatment. Further studies are needed to confirm the clinical relevance of this discovery. Below, we will discuss the scientific evidence of the role of the microbiome in seizure disorders, the impact of the ketogenic diet on the intestinal microbiota as well as the interactions described between commonly used antiepileptic drugs and intestinal microbial communities. We also discuss the potential of modulators of the gut microbiota as possible future anti-seizure therapeutics.
Collapse
Affiliation(s)
- Maria Dahlin
- Neuropediatric Department, Astrid Lindgren Children's Hospital, Karolinska Hospital, Stockholm, Sweden
| | - Stefanie Prast-Nielsen
- Center for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
45
|
Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, Weinberger A, Fu J, Wijmenga C, Zhernakova A, Segal E. Structural variation in the gut microbiome associates with host health. Nature 2019; 568:43-48. [PMID: 30918406 DOI: 10.1038/s41586-019-1065-y] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.
Collapse
Affiliation(s)
- David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. .,Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA.
| | - Tal Korem
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
46
|
The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy. NPJ Biofilms Microbiomes 2019; 5:5. [PMID: 30701077 PMCID: PMC6344533 DOI: 10.1038/s41522-018-0073-2] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2018] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota has been linked to various neurological disorders via the gut–brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer’s, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after 3 months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing, both taxonomic and functional profiles were established. Here we report that alpha diversity is not changed significantly during the diet, but differences in both taxonomic and functional composition are detected. Relative abundance of bifidobacteria as well as E. rectale and Dialister is significantly diminished during the intervention. An increase in relative abundance of E. coli is observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicates that bifidobacteria and Escherichia are important contributors to the observed functional shifts. As relative abundance of health-promoting, fiber-consuming bacteria becomes less abundant during KD, we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD. The ketogenic diet changes both the relative abundance of gut microbiota and their metabolic activities. The diet forces a shift from carbohydrates to ketones as a primary energy source and has demonstrated efficacy in reducing epileptic seizures in children. After animal models implicated gut microbiota in this amelioration, Stefanie Prast-Nielsen, of Sweden’s Karolinska Institutet, and her team sequenced microbiotic DNA of fecal samples from 12 children with epilepsy before and after 3 months on a ketogenic diet. Changes included reductions in the numbers of Bifidobacterium and an increase in Escherichia coli. Carbohydrate metabolism significantly changed after 3 months on the diet. Some reductions raise questions about the diet’s potential impact on gut and overall health. More studies are also needed to discern the mechanistic impact of these changes on seizure activity.
Collapse
|
47
|
Guillén Y, Noguera-Julian M, Rivera J, Casadellà M, Zevin AS, Rocafort M, Parera M, Rodríguez C, Arumí M, Carrillo J, Mothe B, Estany C, Coll J, Bravo I, Herrero C, Saz J, Sirera G, Torrella A, Navarro J, Crespo M, Negredo E, Brander C, Blanco J, Calle ML, Klatt NR, Clotet B, Paredes R. Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection. Mucosal Immunol 2019; 12:232-246. [PMID: 30171206 DOI: 10.1038/s41385-018-0083-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/03/2018] [Accepted: 08/08/2018] [Indexed: 02/04/2023]
Abstract
Human immunodeficiency virus (HIV)-1 infection causes severe gut and systemic immune damage, but its effects on the gut microbiome remain unclear. Previous shotgun metagenomic studies in HIV-negative subjects linked low-microbial gene counts (LGC) to gut dysbiosis in diseases featuring intestinal inflammation. Using a similar approach in 156 subjects with different HIV-1 phenotypes, we found a strong, independent, dose-effect association between nadir CD4+ T-cell counts and LGC. As in other diseases involving intestinal inflammation, the gut microbiomes of subjects with LGC were enriched in gram-negative Bacteroides, acetogenic bacteria and Proteobacteria, which are able to metabolize reactive oxygen and nitrogen species; and were depleted in oxygen-sensitive methanogenic archaea and sulfate-reducing bacteria. Interestingly, subjects with LGC also showed increased butyrate levels in direct fecal measurements, consistent with enrichment in Roseburia intestinalis despite reductions in other butyrate producers. The microbiomes of subjects with LGC were also enriched in bacterial virulence factors, as well as in genes associated with beta-lactam, lincosamide, tetracycline, and macrolide resistance. Thus, low nadir CD4+ T-cell counts, rather than HIV-1 serostatus per se, predict the presence of gut dysbiosis in HIV-1 infected subjects. Such dysbiosis does not display obvious HIV-specific features; instead, it shares many similarities with other diseases featuring gut inflammation.
Collapse
Affiliation(s)
- Yolanda Guillén
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Marc Noguera-Julian
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain
| | - Javier Rivera
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain
| | - Maria Casadellà
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Alexander S Zevin
- University of Washington, 3018 Western Avenue, Seattle, WA, 98121, USA
| | - Muntsa Rocafort
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Mariona Parera
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Cristina Rodríguez
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Marçal Arumí
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Jorge Carrillo
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Beatriz Mothe
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain.,Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Carla Estany
- Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Josep Coll
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Isabel Bravo
- Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Cristina Herrero
- Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Jorge Saz
- BCN Checkpoint, Carrer del Comte Borrell, 164, Barcelona, 08015, Catalonia, Spain
| | - Guillem Sirera
- Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Ariadna Torrella
- Infectious Diseases Unit, Hospital Universitari Vall d'Hebrón, Passeig de la Vall d'Hebrón, 119-129, Barcelona, 08035, Catalonia, Spain
| | - Jordi Navarro
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.,Infectious Diseases Unit, Hospital Universitari Vall d'Hebrón, Passeig de la Vall d'Hebrón, 119-129, Barcelona, 08035, Catalonia, Spain
| | - Manuel Crespo
- Infectious Diseases Unit, Internal Medicine Department, Complexo Hospitalario Universitario, Vigo. IIS Galicia Sur, Estrada de Clara Campoamor, 341, Vigo, 36312, Pontevedra, Spain
| | - Eugènia Negredo
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain.,Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Christian Brander
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Julià Blanco
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain
| | - Maria Luz Calle
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain
| | - Nichole R Klatt
- University of Washington, 3018 Western Avenue, Seattle, WA, 98121, USA
| | - Bonaventura Clotet
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain.,Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain
| | - Roger Paredes
- irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain. .,Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain. .,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, Vic, 08500, Catalonia, Spain. .,Infectious Diseases Service & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, Badalona, 08916, Catalonia, Spain.
| |
Collapse
|
48
|
Huang T, Zhang M, Tong X, Chen J, Yan G, Fang S, Guo Y, Yang B, Xiao S, Chen C, Huang L, Ai H. Microbial communities in swine lungs and their association with lung lesions. Microb Biotechnol 2018; 12:289-304. [PMID: 30556308 PMCID: PMC6389860 DOI: 10.1111/1751-7915.13353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Under natural farming, environmental pathogenic microorganisms may invade and affect swine lungs, further resulting in lung lesions. However, few studies on swine lung microbiota and their potential relationship with lung lesions were reported. Here, we sampled 20 pigs from a hybrid herd raised under natural conditions; we recorded a lung‐lesion phenotype and investigated lung microbial communities by sequencing the V3‐V4 region of 16S rRNA gene for each individual. We found reduced microbial diversity but more biomass in the severe‐lesion lungs. Methylotenera, Prevotella, Sphingobium and Lactobacillus were the prominent bacteria in the healthy lungs, while Mycoplasma, Ureaplasma, Sphingobium, Haemophilus and Phyllobacterium were the most abundant microbes in the severe‐lesion lungs. Notably, we identified 64 lung‐lesion‐associated OTUs, of which two classified to Mycoplasma were positively associated with lung lesions and 62 showed negative association including thirteen classified to Prevotella and six to Ruminococcus. Cross‐validation analysis showed that lung microbiota explained 23.7% phenotypic variance of lung lesions, suggesting that lung microbiota had large effects on promoting lung healthy. Furthermore, 22 KEGG pathways correlated with lung lesions were predicted. Altogether, our findings improve the knowledge about swine lung microbial communities and give insights into the relationship between lung microbiota and lung lesions.
Collapse
Affiliation(s)
- Tao Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Mingpeng Zhang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinkai Tong
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiaqi Chen
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guorong Yan
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shaoming Fang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yuanmei Guo
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Congying Chen
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lusheng Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huashui Ai
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| |
Collapse
|
49
|
Cai Z, Yao Z, Li Y, Xi Z, Bourtzis K, Zhao Z, Bai S, Zhang H. Intestinal probiotics restore the ecological fitness decline of Bactrocera dorsalis by irradiation. Evol Appl 2018; 11:1946-1963. [PMID: 30459840 PMCID: PMC6231467 DOI: 10.1111/eva.12698] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 08/09/2018] [Accepted: 08/15/2018] [Indexed: 12/18/2022] Open
Abstract
The sterile insect technique (SIT) as an eco-friendly and reliable strategy has been used to control populations of insect pests of agricultural, veterinary and human health importance. Successful applications of SIT rely on the high-level ecological fitness of sterile males. A suitable and stable gut microbiome can contribute to the ecological fitness of insect by influencing their physiology, biochemistry and development processes. Here, we show that a shift in the gut bacterial composition and structure by sterilizing irradiation, characterized by a decrease in the major gut microbiota community Enterobacteriaceae, an expansion of the minor members (e.g., Bacillaceae) and a higher richness and diversity, is tightly linked to radiation-induced ecological fitness (male mating competitiveness, flight capacity, survival rate and life span) decline in Bactrocera dorsalis (Hendel) sterile males. Function prediction of gut microbiota indicated that changes in microbiome taxonomy tend to drive microbiome functional shifts. A higher nutrient consumption of the flourishing minor gut microbiota may cause a decline in nutrients and energy metabolic activity of host and then result in the reduced ecological fitness of irradiated flies. Furthermore, we found that a gut bacterial strain Klebsiella oxytoca (BD177) can restore ecological fitness by improving food intake and increasing haemolymph sugar and amino acid levels of irradiated B. dorsalis flies. Our findings suggest that gut symbiont-based probiotics can be used as agents for reversing radiation-induced ecological fitness decrease.
Collapse
Affiliation(s)
- Zhaohui Cai
- State Key Laboratory of Agricultural MicrobiologyKey Laboratory of Horticultural Plant Biology (MOE)China‐Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zhichao Yao
- State Key Laboratory of Agricultural MicrobiologyKey Laboratory of Horticultural Plant Biology (MOE)China‐Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yushan Li
- State Key Laboratory of Agricultural MicrobiologyKey Laboratory of Horticultural Plant Biology (MOE)China‐Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zhiyong Xi
- Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingMichigan
| | - Kostas Bourtzis
- Insect Pest Control LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreViennaAustria
| | - Zheng Zhao
- State Key Laboratory of Agricultural MicrobiologyKey Laboratory of Horticultural Plant Biology (MOE)China‐Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shuai Bai
- State Key Laboratory of Agricultural MicrobiologyKey Laboratory of Horticultural Plant Biology (MOE)China‐Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Hongyu Zhang
- State Key Laboratory of Agricultural MicrobiologyKey Laboratory of Horticultural Plant Biology (MOE)China‐Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
50
|
Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer. PLoS One 2018; 13:e0207002. [PMID: 30412600 PMCID: PMC6226189 DOI: 10.1371/journal.pone.0207002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/23/2018] [Indexed: 12/15/2022] Open
Abstract
Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa. The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear. In this study, we systematically analyzed previously published 16S rRNA sequence data from CRC patients with matched tumor:tumor-adjacent biopsies (n = 294 pairs, n = 588 biospecimens) and matched tumor biopsy:fecal pairs (n = 42 pairs, n = 84 biospecimens). Procrustes analyses, random effects regression, random forest (RF) modeling, and inferred functional pathway analyses were conducted to assess community similarity and microbial diversity across heterogeneous patient groups and studies. Our results corroborate previously reported association of increased Fusobacterium with tumor biopsies. Parvimonas and Streptococcus abundances were also elevated while Faecalibacterium and Ruminococcaceae abundances decreased in tumors relative to tumor-adjacent biopsies and stool samples from the same case. With the exception of these limited taxa, the majority of findings from individual studies were not confirmed by other 16S rRNA gene-based datasets. RF models comparing tumor and tumor-adjacent specimens yielded an area under curve (AUC) of 64.3%, and models of tumor biopsies versus fecal specimens exhibited an AUC of 82.5%. Although some taxa were shared between fecal and tumor samples, their relative abundances varied substantially. Inferred functional analysis identified potential differences in branched amino acid and lipid metabolism. Microbial markers that reliably occur in tumor tissue can have implications for microbiome based and microbiome targeting therapeutics for CRC.
Collapse
|