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Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus). mSystems 2024; 9:e0010824. [PMID: 38975760 PMCID: PMC11334461 DOI: 10.1128/msystems.00108-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/01/2024] [Indexed: 07/09/2024] Open
Abstract
Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change. IMPORTANCE Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.
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Affiliation(s)
- Cassandra Tang-Wing
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Katherine Makowski
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Daira Melendez
- Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Keith Jenné
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
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2
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Lekbua A, Thiruppathy D, Coker J, Weng Y, Askarian F, Kousha A, Marotz C, Hauw A, Nizet V, Zengler K. SkinCom, a synthetic skin microbial community, enables reproducible investigations of the human skin microbiome. CELL REPORTS METHODS 2024; 4:100832. [PMID: 39111313 DOI: 10.1016/j.crmeth.2024.100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/30/2024] [Accepted: 07/12/2024] [Indexed: 08/22/2024]
Abstract
Existing models of the human skin have aided our understanding of skin health and disease. However, they currently lack a microbial component, despite microbes' demonstrated connections to various skin diseases. Here, we present a robust, standardized model of the skin microbial community (SkinCom) to support in vitro and in vivo investigations. Our methods lead to the formation of an accurate, reproducible, and diverse community of aerobic and anaerobic bacteria. Subsequent testing of SkinCom on the dorsal skin of mice allowed for DNA and RNA recovery from both the applied SkinCom and the dorsal skin, highlighting its practicality for in vivo studies and -omics analyses. Furthermore, 66% of the responses to common cosmetic chemicals in vitro were in agreement with a human trial. Therefore, SkinCom represents a valuable, standardized tool for investigating microbe-metabolite interactions and facilitates the experimental design of in vivo studies targeting host-microbe relationships.
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Affiliation(s)
- Asama Lekbua
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Deepan Thiruppathy
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joanna Coker
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yuhan Weng
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fatemeh Askarian
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Armin Kousha
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clarisse Marotz
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amber Hauw
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor Nizet
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karsten Zengler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Gao FZ, Hu LX, Liu YS, Qiao LK, Chen ZY, Su JQ, He LY, Bai H, Zhu YG, Ying GG. Unveiling the overlooked small-sized microbiome in river ecosystems. WATER RESEARCH 2024; 265:122302. [PMID: 39178591 DOI: 10.1016/j.watres.2024.122302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/12/2024] [Accepted: 08/18/2024] [Indexed: 08/26/2024]
Abstract
Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Li-Xin Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Lu-Kai Qiao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
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Schulkers Escalante K, Bai-Tong SS, Allard SM, Ecklu-Mensah G, Sanchez C, Song SJ, Gilbert J, Bode L, Dorrestein P, Knight R, Gonzalez DJ, Leibel SA, Leibel SL. The impact of breastfeeding on the preterm infant's microbiome and metabolome: a pilot study. Pediatr Res 2024:10.1038/s41390-024-03440-9. [PMID: 39138352 DOI: 10.1038/s41390-024-03440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/23/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND Human milk is unquestionably beneficial for preterm infants. We investigated how the transition from tube to oral/breastfeeding impacts the preterm infants' oral and gut microbiome and metabolome. METHODS We analyzed stool, saliva, and milk samples collected from a cohort of preterm infants enrolled in the MAP Study, a prospective observational trial. The microbiome and metabolome of the samples were analyzed from 4 longitudinal sample time points, 2 during tube feeds only and 2 after the initiation of oral/breastfeeding. RESULTS We enrolled 11 mother-infant dyads (gestational age = 27.9 (23.4-32.2)) and analyzed a total of 39 stool, 44 saliva, and 43 milk samples over 4 timepoints. In saliva samples, there was a shift towards increased Streptococcus and decreased Staphylococcus after oral feeding/breastfeeding initiation (p < 0.05). Milk sample metabolites were strongly influenced by the route of feeding and milk type (p < 0.05) and represented the pathways of Vitamin E metabolism, Vitamin B12 metabolism, and Tryptophan metabolism. CONCLUSION Our analysis demonstrated that the milk and preterm infant's saliva microbiome and metabolome changed over the course of the first four to 5 months of life, coinciding with the initiation of oral/breastfeeds. IMPACT The microbiome and metabolome is altered in the infant's saliva but not their stool, and in mother's milk when feeds are transitioned from tube to oral/breastfeeding. We assessed the relationship between the gut and oral microbiome/metabolome with the milk microbiome/metabolome over a longitudinal period of time in preterm babies. Metabolites that changed in the infants saliva after the initiation of oral feeds have the potential to be used as biomarkers for disease risk.
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Affiliation(s)
| | - Shiyu S Bai-Tong
- Department of Pediatrics, University of California San Diego, Rady Children's Hospital, La Jolla, CA, USA
| | - Sarah M Allard
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Concepcion Sanchez
- Department of Pharmacology and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jack Gilbert
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA, USA
| | - Pieter Dorrestein
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - David J Gonzalez
- Department of Pharmacology and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sydney A Leibel
- Department of Pediatrics, University of California San Diego, Rady Children's Hospital, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, Rady Children's Hospital, La Jolla, CA, USA.
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5
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res 2024; 52:e63. [PMID: 38909293 DOI: 10.1093/nar/gkae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Melanie B Prentice
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Gene S Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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6
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Kostenko A, Zuffa S, Zhi H, Mildau K, Raffatellu M, Dorrestein PC, Aron AT. Dietary iron intake has long-term effects on the fecal metabolome and microbiome. Metallomics 2024; 16:mfae033. [PMID: 38992131 PMCID: PMC11272056 DOI: 10.1093/mtomcs/mfae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/10/2024] [Indexed: 07/13/2024]
Abstract
Iron is essential for life, but its imbalances can lead to severe health implications. Iron deficiency is the most common nutrient disorder worldwide, and iron dysregulation in early life has been found to cause long-lasting behavioral, cognitive, and neural effects. However, little is known about the effects of dietary iron on gut microbiome function and metabolism. In this study, we sought to investigate the impact of dietary iron on the fecal metabolome and microbiome by using mice fed with three diets with different iron content: an iron deficient, an iron sufficient (standard), and an iron overload diet for 7 weeks. Additionally, we sought to understand whether any observed changes would persist past the 7-week period of diet intervention. To assess this, all feeding groups were switched to a standard diet, and this feeding continued for an additional 7 weeks. Analysis of the fecal metabolome revealed that iron overload and deficiency significantly alter levels of peptides, nucleic acids, and lipids, including di- and tri-peptides containing branched-chain amino acids, inosine and guanosine, and several microbial conjugated bile acids. The observed changes in the fecal metabolome persist long after the switch back to a standard diet, with the cecal gut microbiota composition and function of each group distinct after the 7-week standard diet wash-out. Our results highlight the enduring metabolic consequences of nutritional imbalances, mediated by both the host and gut microbiome, which persist after returning to the original standard diets.
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Affiliation(s)
- Anastasiia Kostenko
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hui Zhi
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kevin Mildau
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Chiba University, UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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7
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Schweickart A, Batra R, Neth BJ, Martino C, Shenhav L, Zhang AR, Shi P, Karu N, Huynh K, Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach C, Dorrestein PC, Knight R, Craft S, Kaddurah-Daouk R, Krumsiek J. Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease. NPJ METABOLIC HEALTH AND DISEASE 2024; 2:15. [PMID: 38962750 PMCID: PMC11216994 DOI: 10.1038/s44324-024-00016-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/16/2024] [Indexed: 07/05/2024]
Abstract
Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored KD's metabolic impact, especially on blood and cerebrospinal fluid (CSF). Our study involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean Ketogenic Diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum and CSF and metagenomics profiling on fecal samples. While the AHAD induced no notable metabolic changes, MMKD led to significant alterations in both serum and CSF. These changes included improved modifiable risk factors, like increased HDL-C and reduced BMI, reversed serum metabolic disturbances linked to AD such as a microbiome-mediated increase in valine levels, and a reduction in systemic inflammation. Additionally, the MMKD was linked to increased amino acid levels in the CSF, a breakdown of branched-chain amino acids (BCAAs), and decreased valine levels. Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. Our findings highlight that MMKD can improve AD-related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood-CSF barrier.
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Affiliation(s)
- Annalise Schweickart
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY USA
| | - Richa Batra
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY USA
| | - Bryan J. Neth
- Department of Neurology, Mayo Clinic, Rochester, MN USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - Liat Shenhav
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY USA
| | - Anru R. Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC USA
| | - Pixu Shi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC USA
| | - Naama Karu
- Tasmanian Independent Metabolomics and Analytical Chemistry Solutions (TIMACS), Hobart, TAS Australia
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC Australia
| | - Peter J. Meikle
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC Australia
| | - Leyla Schimmel
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC USA
| | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, Bioengineering, University of California San Diego, La Jolla, CA USA
| | - Alzheimer’s Gut Microbiome Project Consortium
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY USA
- Department of Neurology, Mayo Clinic, Rochester, MN USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC USA
- Tasmanian Independent Metabolomics and Analytical Chemistry Solutions (TIMACS), Hobart, TAS Australia
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC Australia
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC USA
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Duke Molecular Physiology Institute, Duke University, Durham, NC USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Departments of Pediatrics, Computer Science and Engineering, Bioengineering, University of California San Diego, La Jolla, CA USA
- Department of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston Salem, NC USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC USA
- Department of Medicine, Duke University, Durham, NC USA
| | - Suzanne Craft
- Department of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston Salem, NC USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC USA
- Department of Medicine, Duke University, Durham, NC USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY USA
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8
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Kopera K, Gromowski T, Wydmański W, Skonieczna-Żydecka K, Muszyńska A, Zielińska K, Wierzbicka-Woś A, Kaczmarczyk M, Kadaj-Lipka R, Cembrowska-Lech D, Januszkiewicz K, Kotfis K, Witkiewicz W, Nalewajska M, Feret W, Marlicz W, Łoniewski I, Łabaj PP, Rydzewska G, Kosciolek T. Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing. Front Microbiol 2024; 15:1342749. [PMID: 38962119 PMCID: PMC11219902 DOI: 10.3389/fmicb.2024.1342749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.
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Affiliation(s)
- Katarzyna Kopera
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Tomasz Gromowski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Witold Wydmański
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Faculty of Mathematics and Computer Science, Jagiellonian University, Kraków, Poland
| | | | - Agata Muszyńska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kinga Zielińska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | | | - Mariusz Kaczmarczyk
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Roland Kadaj-Lipka
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Danuta Cembrowska-Lech
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | | | - Katarzyna Kotfis
- Department of Anesthesiology, Intensive Care and Pain Management, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Wiktoria Feret
- Clinical Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Marlicz
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Igor Łoniewski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | - Paweł P. Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Grażyna Rydzewska
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Tomasz Kosciolek
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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9
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Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol 2024; 42:768-777. [PMID: 37500914 PMCID: PMC10818028 DOI: 10.1038/s41587-023-01868-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Phylogenetic trees provide a framework for organizing evolutionary histories across the tree of life and aid downstream comparative analyses such as metagenomic identification. Methods that rely on single-marker genes such as 16S rRNA have produced trees of limited accuracy with hundreds of thousands of organisms, whereas methods that use genome-wide data are not scalable to large numbers of genomes. We introduce updating trees using divide-and-conquer (uDance), a method that enables updatable genome-wide inference using a divide-and-conquer strategy that refines different parts of the tree independently and can build off of existing trees, with high accuracy and scalability. With uDance, we infer a species tree of roughly 200,000 genomes using 387 marker genes, totaling 42.5 billion amino acid residues.
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Affiliation(s)
- Metin Balaban
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
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10
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McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol 2024; 42:715-718. [PMID: 37500913 PMCID: PMC10818020 DOI: 10.1038/s41587-023-01845-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/25/2023] [Indexed: 07/29/2023]
Abstract
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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Affiliation(s)
- Daniel McDonald
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James T Morton
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Giorgia Nicolaou
- Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Søren M Karst
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Todd DeSantis
- Department of Informatics, Second Genome, Brisbane, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Andrew Bartko
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Aki S Havulinna
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | | | - Susan Cheng
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Mohit Jain
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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11
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Gheorghe CE, Leigh SJ, Tofani GSS, Bastiaanssen TFS, Lyte JM, Gardellin E, Govindan A, Strain C, Martinez-Herrero S, Goodson MS, Kelley-Loughnane N, Cryan JF, Clarke G. The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut. Cell Rep 2024; 43:114079. [PMID: 38613781 DOI: 10.1016/j.celrep.2024.114079] [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: 01/23/2023] [Revised: 02/09/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024] Open
Abstract
Chronic stress disrupts microbiota-gut-brain axis function and is associated with altered tryptophan metabolism, impaired gut barrier function, and disrupted diurnal rhythms. However, little is known about the effects of acute stress on the gut and how it is influenced by diurnal physiology. Here, we used germ-free and antibiotic-depleted mice to understand how microbiota-dependent oscillations in tryptophan metabolism would alter gut barrier function at baseline and in response to an acute stressor. Cecal metabolomics identified tryptophan metabolism as most responsive to a 15-min acute stressor, while shotgun metagenomics revealed that most bacterial species exhibiting rhythmicity metabolize tryptophan. Our findings highlight that the gastrointestinal response to acute stress is dependent on the time of day and the microbiome, with a signature of stress-induced functional alterations in the ileum and altered tryptophan metabolism in the colon.
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Affiliation(s)
- Cassandra E Gheorghe
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Sarah-Jane Leigh
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Gabriel S S Tofani
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Joshua M Lyte
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Elisa Gardellin
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, T12 CY82 Cork, Ireland
| | - Ashokkumar Govindan
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Teagasc Moorepark Food Research Centre, Fermoy Co, P61 C996 Cork, Ireland
| | - Conall Strain
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Teagasc Moorepark Food Research Centre, Fermoy Co, P61 C996 Cork, Ireland
| | - Sonia Martinez-Herrero
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Michael S Goodson
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45324, USA
| | - Nancy Kelley-Loughnane
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45324, USA
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, T12 CY82 Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, T12 CY82 Cork, Ireland.
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12
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Goldman SL, Sanders JG, Sprockett DD, Landers A, Yan W, Moeller AH. Hackflex library preparation enables low-cost metagenomic profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590092. [PMID: 38712258 PMCID: PMC11071439 DOI: 10.1101/2024.04.23.590092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.
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Affiliation(s)
- Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Abigail Landers
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540
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13
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Dokoshi T, Chen Y, Cavagnero KJ, Rahman G, Hakim D, Brinton S, Schwarz H, Brown EA, O'Neill A, Nakamura Y, Li F, Salzman NH, Knight R, Gallo RL. Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice. Nat Commun 2024; 15:3009. [PMID: 38589392 PMCID: PMC11001995 DOI: 10.1038/s41467-024-47072-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
The composition of the microbial community in the intestine may influence the functions of distant organs such as the brain, lung, and skin. These microbes can promote disease or have beneficial functions, leading to the hypothesis that microbes in the gut explain the co-occurrence of intestinal and skin diseases. Here, we show that the reverse can occur, and that skin directly alters the gut microbiome. Disruption of the dermis by skin wounding or the digestion of dermal hyaluronan results in increased expression in the colon of the host defense genes Reg3 and Muc2, and skin wounding changes the composition and behavior of intestinal bacteria. Enhanced expression Reg3 and Muc2 is induced in vitro by exposure to hyaluronan released by these skin interventions. The change in the colon microbiome after skin wounding is functionally important as these bacteria penetrate the intestinal epithelium and enhance colitis from dextran sodium sulfate (DSS) as seen by the ability to rescue skin associated DSS colitis with oral antibiotics, in germ-free mice, and fecal microbiome transplantation to unwounded mice from mice with skin wounds. These observations provide direct evidence of a skin-gut axis by demonstrating that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut microbiome.
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Affiliation(s)
- Tatsuya Dokoshi
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Yang Chen
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Kellen J Cavagnero
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Hakim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Samantha Brinton
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Hana Schwarz
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth A Brown
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Alan O'Neill
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Yoshiyuki Nakamura
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Fengwu Li
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Nita H Salzman
- Department of Pediatrics, Division of Gastroenterology and Center for Microbiome Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA.
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14
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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024; 43:1127-1148. [PMID: 38396294 PMCID: PMC10997506 DOI: 10.1038/s41388-024-02974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.
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Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, 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
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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15
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Şapcı AOB, Rachtman E, Mirarab S. CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing. Bioinformatics 2024; 40:btae150. [PMID: 38492564 PMCID: PMC10985673 DOI: 10.1093/bioinformatics/btae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/17/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024] Open
Abstract
MOTIVATION Taxonomic classification of short reads and taxonomic profiling of metagenomic samples are well-studied yet challenging problems. The presence of species belonging to groups without close representation in a reference dataset is particularly challenging. While k-mer-based methods have performed well in terms of running time and accuracy, they tend to have reduced accuracy for such novel species. Thus, there is a growing need for methods that combine the scalability of k-mers with increased sensitivity. RESULTS Here, we show that using locality-sensitive hashing (LSH) can increase the sensitivity of the k-mer-based search. Our method, which combines LSH with several heuristics techniques including soft lowest common ancestor labeling and voting, is more accurate than alternatives in both taxonomic classification of individual reads and abundance profiling. AVAILABILITY AND IMPLEMENTATION CONSULT-II is implemented in C++, and the software, together with reference libraries, is publicly available on GitHub https://github.com/bo1929/CONSULT-II.
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Affiliation(s)
- Ali Osman Berk Şapcı
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, CA 92093, United States
| | - Eleonora Rachtman
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, CA 92093, United States
| | - Siavash Mirarab
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, CA 92093, United States
- Department of Electrical and Computer Engineering, University of California, San Diego, CA 92093, United States
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16
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Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R. Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585820. [PMID: 38562901 PMCID: PMC10983923 DOI: 10.1101/2024.03.19.585820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive disorder (MDD), as defined by DSM-IV or V criteria. The study also examined the influence of medication use, particularly antidepressants and/or anxiolytics, classified through the Anatomical Therapeutic Chemical (ATC) Classification System, on the gut microbiota. Both 16S rRNA gene amplicon sequencing and shallow shotgun sequencing were performed on DNA extracted from 666 fecal samples from the Tulsa-1000 and NeuroMAP CoBRE cohorts. The results highlight the significant influence of medication use; antidepressant use is associated with significant differences in gut microbiota beta diversity and has a larger effect size than NPD diagnosis. Next, specific microbes were associated with ANXD and MDD, highlighting their potential for non-pharmacological intervention. Finally, the study demonstrated the capability of Random Forest classifiers to predict diagnoses of NPD and medication use from microbial profiles, suggesting a promising direction for the use of gut microbiota as biomarkers for NPD. The findings suggest that future research on the gut microbiota's role in NPD and its interactions with pharmacological treatments are needed.
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Affiliation(s)
- Amanda Hazel Dilmore
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Rayus Kuplicki
- Laureate Institute for Brain Research, Tulsa, Oklahoma, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Megha Kumar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Tyakht
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colette Blach
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Boadie W. Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Sudeepa Bhattacharyya
- Department of Biological Sciences, Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA
| | | | - Pooja Mandaviya
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Rima Kaddaruh-Dauok
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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17
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Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey FE, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk RF, Bendlin BB, Hertel J, Thiele I. Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Sci Rep 2024; 14:6095. [PMID: 38480804 PMCID: PMC10937638 DOI: 10.1038/s41598-024-55960-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
In this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimer's disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilised whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalised whole-body metabolic models. Notably, AD individuals displayed diminished formate microbial secretion in these models. Additionally, we identified specific reactions responsible for the production of formate in the host, and interestingly, these reactions were linked to genes that have correlations with AD. This study suggests formate as a possible early AD marker and highlights genetic and microbiome contributions to its production. The reduced formate secretion and its genetic associations point to a complex connection between gut microbiota and AD. This holistic understanding might pave the way for novel diagnostic and therapeutic avenues in AD management.
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Affiliation(s)
- Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
- Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Ann-Kristin Henning
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Maria A Ulmer
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tim Hensen
- School of Medicine, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioural Sciences, Duke University, Durham, NC, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Kathrin Budde
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Corinne D Engelman
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Hans-Jörgen Grabe
- German Center of Neurodegenerative Diseases (DZNE), Rostock/Greifswald, Germany
| | - Margo B Heston
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Sterling Johnson
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ingo Kilimann
- German Center of Neurodegenerative Diseases (DZNE), Rostock, Germany
- Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
| | - Olive Peters
- German Center of Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xiao Wang
- Department of Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Eike Jakob Spruth
- German Center of Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry and Psychotherapy, Charité, Berlin, Germany
| | - Anja Schneider
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Klaus Fliessbach
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Jens Wiltfang
- German Center of Neurodegenerative Diseases (DZNE), Goettingen, Germany
- Department of Psychiatry and Psychotherapy, University of Goettingen, Goettingen, Germany
- Neurosciences and Signaling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Niels Hansen
- Department of Psychiatry and Psychotherapy, University of Goettingen, Goettingen, Germany
| | - Wenzel Glanz
- German Center of Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Katharina Buerger
- German Center of Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Daniel Janowitz
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Christoph Laske
- German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Section for Dementia Research, Hertie Institute for Clinical Brain Research, Tübingen, Germany
- Section for Dementia Research, Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Matthias H Munk
- German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Section for Dementia Research, Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Annika Spottke
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Nina Roy
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Stefan Teipel
- German Center of Neurodegenerative Diseases (DZNE), Rostock, Germany
- Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Engineering, University of California San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | | | - Barbara B Bendlin
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Johannes Hertel
- School of Medicine, University of Galway, Galway, Ireland.
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany.
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland.
- The Ryan Institute, University of Galway, Galway, Ireland.
- School of Microbiology, University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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18
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Gao FZ, He LY, He LX, Bai H, Zhang M, Chen ZY, Qiao LK, Liu YS, Ying GG. Swine farming shifted the gut antibiotic resistome of local people. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133082. [PMID: 38016315 DOI: 10.1016/j.jhazmat.2023.133082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China.
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Lu-Kai Qiao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China.
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19
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Wang X, Li J, Zheng J, Zhao L, Ruan C, Zhang D, Pan X. Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169976. [PMID: 38199380 DOI: 10.1016/j.scitotenv.2024.169976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.
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Affiliation(s)
- Xiaonan Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Hangzhou 310015, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou 221116, China; Shaoxing Research Institute of Zhejiang University of Technology, Shaoxing 312000, China
| | - Jiahao Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jieyan Zheng
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lanxin Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenghao Ruan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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20
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Gao FZ, He LY, Liu YS, Zhao JL, Zhang T, Ying GG. Integrating global microbiome data into antibiotic resistance assessment in large rivers. WATER RESEARCH 2024; 250:121030. [PMID: 38113599 DOI: 10.1016/j.watres.2023.121030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Rivers are important in spreading antimicrobial resistance (AMR). Assessing AMR risk in large rivers is challenged by large spatial scale and numerous contamination sources. Integrating river resistome data into a global framework may help addressing this difficulty. Here, we conducted an omics-based assessment of AMR in a large river (i.e. the Pearl River in China) with global microbiome data. Results showed that antibiotic resistome in river water and sediment was more diversified than that in other rivers, with contamination levels in some river reaches higher than global baselines. Discharge of WWTP effluent and landfill waste drove AMR prevalence in the river, and the resistome level was highly associated with human and animal sources. Detection of 54 risk rank I ARGs and emerging mobilizable mcr and tet(X) highlighted AMR risk in the river reaches with high human population density and livestock pollution. Florfenicol-resistant floR therein deserved priority concerns due to its high detection frequency, dissimilar phylogenetic distance, mobilizable potential, and presence in multiple pathogens. Co-sharing of ARGs across taxonomic ranks implied their transfer potentials in the community. By comparing with global genomic data, we found that Burkholderiaceae, Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae were important potential ARG-carrying bacteria in the river, and WHO priority carbapenem-resistant Enterobacteriaceae, A. baumannii and P. aeruginosa should be included in future surveillance. Collectively, the findings from this study provide an omics-benchmarked assessment strategy for public risk associated with AMR in large rivers.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
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21
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Linnehan BK, Kodera SM, Allard SM, Brodie EC, Allaband C, Knight R, Lutz HL, Carroll MC, Meegan JM, Jensen ED, Gilbert JA. Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing. J Appl Microbiol 2024; 135:lxae026. [PMID: 38305096 PMCID: PMC10853691 DOI: 10.1093/jambio/lxae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/28/2023] [Accepted: 01/31/2024] [Indexed: 02/03/2024]
Abstract
AIMS Gastrointestinal disease is a leading cause of morbidity in bottlenose dolphins (Tursiops truncatus) under managed care. Fecal microbiota transplantation (FMT) holds promise as a therapeutic tool to restore gut microbiota without antibiotic use. This prospective clinical study aimed to develop a screening protocol for FMT donors to ensure safety, determine an effective FMT administration protocol for managed dolphins, and evaluate the efficacy of FMTs in four recipient dolphins. METHODS AND RESULTS Comprehensive health monitoring was performed on donor and recipient dolphins. Fecal samples were collected before, during, and after FMT therapy. Screening of donor and recipient fecal samples was accomplished by in-house and reference lab diagnostic tests. Shotgun metagenomics was used for sequencing. Following FMT treatment, all four recipient communities experienced engraftment of novel microbial species from donor communities. Engraftment coincided with resolution of clinical signs and a sustained increase in alpha diversity. CONCLUSION The donor screening protocol proved to be safe in this study and no adverse effects were observed in four recipient dolphins. Treatment coincided with improvement in clinical signs.
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Affiliation(s)
| | - Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
| | - Erin C Brodie
- National Marine Mammal Foundation, San Diego, CA 92106, United States
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, United States
- Department of Medicine, University of California San Diego, La Jolla, CA 92161, United States
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Holly L Lutz
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, United States
| | | | - Jennifer M Meegan
- National Marine Mammal Foundation, San Diego, CA 92106, United States
| | - Eric D Jensen
- U.S. Navy Marine Mammal Program, Naval Information Warfare Center Pacific, San Diego, CA 92106, United States
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, United States
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22
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Valencia EM, Maki KA, Dootz JN, Barb JJ. Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines. Sci Data 2024; 11:81. [PMID: 38233447 PMCID: PMC10794705 DOI: 10.1038/s41597-023-02877-7] [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: 05/26/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.
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Affiliation(s)
- E Michael Valencia
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA
| | - Katherine A Maki
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA
| | - Jennifer N Dootz
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Jennifer J Barb
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA.
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23
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Luo K, Chen GC, Zhang Y, Moon JY, Xing J, Peters BA, Usyk M, Wang Z, Hu G, Li J, Selvin E, Rebholz CM, Wang T, Isasi CR, Yu B, Knight R, Boerwinkle E, Burk RD, Kaplan RC, Qi Q. Variant of the lactase LCT gene explains association between milk intake and incident type 2 diabetes. Nat Metab 2024; 6:169-186. [PMID: 38253929 PMCID: PMC11097298 DOI: 10.1038/s42255-023-00961-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024]
Abstract
Cow's milk is frequently included in the human diet, but the relationship between milk intake and type 2 diabetes (T2D) remains controversial. Here, using data from the Hispanic Community Health Study/Study of Latinos, we show that in both sexes, higher milk intake is associated with lower risk of T2D in lactase non-persistent (LNP) individuals (determined by a variant of the lactase LCT gene, single nucleotide polymorphism rs4988235 ) but not in lactase persistent individuals. We validate this finding in the UK Biobank. Further analyses reveal that among LNP individuals, higher milk intake is associated with alterations in gut microbiota (for example, enriched Bifidobacterium and reduced Prevotella) and circulating metabolites (for example, increased indolepropionate and reduced branched-chain amino acid metabolites). Many of these metabolites are related to the identified milk-associated bacteria and partially mediate the association between milk intake and T2D in LNP individuals. Our study demonstrates a protective association between milk intake and T2D among LNP individuals and a potential involvement of gut microbiota and blood metabolites in this association.
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Affiliation(s)
- Kai Luo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Guo-Chong Chen
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Nutrition and Food Hygiene, MOE Key Laboratory of Geriatric Diseases and Immunology, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, China
| | - Yanbo Zhang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiaqian Xing
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gang Hu
- Chronic Disease Epidemiology Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Jun Li
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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24
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Eiamsam-Ang T, Tadee P, Buddhasiri S, Chuammitri P, Kittiwan N, Pascoe B, Patchanee P. Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes. J Med Microbiol 2024; 73. [PMID: 38230911 DOI: 10.1099/jmm.0.001787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.
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Affiliation(s)
- Thanaporn Eiamsam-Ang
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Songphon Buddhasiri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Phongsakorn Chuammitri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Nattinee Kittiwan
- Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang, Thailand
| | - Ben Pascoe
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Ineos Oxford Istitute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Prapas Patchanee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
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25
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Goldman SL, Sanders JG, Sprockett DD, Landers A, Yan W, Moeller AH. Hackflex library preparation enables low-cost metagenomic profiling. ISME COMMUNICATIONS 2024; 4:ycae075. [PMID: 38912052 PMCID: PMC11190725 DOI: 10.1093/ismeco/ycae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/25/2024]
Abstract
Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.
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Affiliation(s)
- Samantha L Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd, Ithaca, NY 14850, United States
- Department of Ecology and Evolutionary Biology, Princeton University, 301 Guyot, Princeton, NJ 08540, United States
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd, Ithaca, NY 14850, United States
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd, Ithaca, NY 14850, United States
| | - Abigail Landers
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd, Ithaca, NY 14850, United States
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd, Ithaca, NY 14850, United States
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd, Ithaca, NY 14850, United States
- Department of Ecology and Evolutionary Biology, Princeton University, 301 Guyot, Princeton, NJ 08540, United States
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26
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Schweickart A, Batra R, Neth BJ, Martino C, Shenhav L, Zhang AR, Shi P, Karu N, Huynh K, Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach C, Dorrestein PC, Knight R, Craft S, Kaddurah-Daouk R, Krumsiek J. A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.27.23298990. [PMID: 38076824 PMCID: PMC10705656 DOI: 10.1101/2023.11.27.23298990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored KD's metabolic impact, especially on blood and cerebrospinal fluid (CSF). Our study involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean-ketogenic diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum and CSF and metagenomics profiling on fecal samples. While the AHAD induced no notable metabolic changes, MMKD led to significant alterations in both serum and CSF. These changes included improved modifiable risk factors, like increased HDL-C and reduced BMI, reversed serum metabolic disturbances linked to AD such as a microbiome-mediated increase in valine levels, and a reduction in systemic inflammation. Additionally, the MMKD was linked to increased amino acid levels in the CSF, a breakdown of branched-chain amino acids (BCAAs), and decreased valine levels. Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. Our findings highlight that MMKD can improve AD-related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood-CSF barrier.
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Affiliation(s)
- Annalise Schweickart
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY 10021, USA
| | - Richa Batra
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY 10021, USA
| | | | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Liat Shenhav
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Anru R. Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Pixu Shi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Naama Karu
- Tasmanian Independent Metabolomics and Analytical Chemistry Solutions (TIMACS), Hobart, 7008 Tasmania, Australia
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia
| | - Peter J. Meikle
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia
| | - Leyla Schimmel
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, Bioengineering, University of California San Diego, La Jolla, CA
| | | | - Suzanne Craft
- Department of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston Salem, NC, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY 10021, USA
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27
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Tang H, Chen X, Huang S, Yin G, Wang X, Shen G. Targeting the gut-microbiota-brain axis in irritable bowel disease to improve cognitive function - recent knowledge and emerging therapeutic opportunities. Rev Neurosci 2023; 34:763-773. [PMID: 36757367 DOI: 10.1515/revneuro-2022-0155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/21/2023] [Indexed: 02/10/2023]
Abstract
The brain-gut axis forms a bidirectional communication system between the gastrointestinal (GI) tract and cognitive brain areas. Disturbances to this system in disease states such as inflammatory bowel disease have consequences for neuronal activity and subsequent cognitive function. The gut-microbiota-brain axis refers to the communication between gut-resident bacteria and the brain. This circuits exists to detect gut microorganisms and relay information to specific areas of the central nervous system (CNS) that in turn, regulate gut physiology. Changes in both the stability and diversity of the gut microbiota have been implicated in several neuronal disorders, including depression, autism spectrum disorder Parkinson's disease, Alzheimer's disease and multiple sclerosis. Correcting this imbalance with medicinal herbs, the metabolic products of dysregulated bacteria and probiotics have shown hope for the treatment of these neuronal disorders. In this review, we focus on recent advances in our understanding of the intricate connections between the gut-microbiota and the brain. We discuss the contribution of gut microbiota to neuronal disorders and the tangible links between diseases of the GI tract with cognitive function and behaviour. In this regard, we focus on irritable bowel syndrome (IBS) given its strong links to brain function and anxiety disorders. This adds to the growing body of evidence supporting targeted therapeutic strategies to modulate the gut microbiota for the treatment of brain/mental-health-related disease.
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Affiliation(s)
- Heyong Tang
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1, Qianjiang Road, 230012 Hefei, Anhui, China
| | - Xiaoqi Chen
- School of Acupuncture and Massage, Anhui University of Chinese Medicine, 230012 Hefei, Anhui, China
| | - Shun Huang
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1, Qianjiang Road, 230012 Hefei, Anhui, China
| | - Gang Yin
- Xin'an School, Anhui University of Chinese Medicine, 230012 Hefei, Anhui, China
| | - Xiyang Wang
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1, Qianjiang Road, 230012 Hefei, Anhui, China
| | - Guoming Shen
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1, Qianjiang Road, 230012 Hefei, Anhui, China
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28
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Yue Y, Read TD, Fedirko V, Satten GA, Hu YJ. Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency. RESEARCH SQUARE 2023:rs.3.rs-3376801. [PMID: 37886529 PMCID: PMC10602108 DOI: 10.21203/rs.3.rs-3376801/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. Methods In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for testing differential abundance at the genus and community levels while overcoming these difficulties. The new method is based on our LOCOM model (Hu et al., 2022), which employs logistic regression for testing taxon differential abundance while remaining robust to experimental bias. To benchmark the performance of Com-2seq, we introduce two ad hoc approaches: applying LOCOM to pooled taxa count data and combining LOCOM p-values from analyzing each dataset separately. Results Our simulation studies indicate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than the two ad hoc approaches. An application of Com-2seq to two real microbiome studies uncovered scientifically plausible findings that would have been missed by analyzing individual datasets. Conclusions Com-2seq performs integrative analysis of 16S and metagenomic sequencing data, which improves statistical efficiency and has the potential to accelerate the search of microbial communities and taxa that are involved in human health and diseases.
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Affiliation(s)
- Ye Yue
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA
| | - Timothy D. Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Veronika Fedirko
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Epidemiology, Emory University, Atlanta, GA, 30322, USA
| | - Glen A. Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA
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29
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Fu T, Huan T, Rahman G, Zhi H, Xu Z, Oh TG, Guo J, Coulter S, Tripathi A, Martino C, McCarville JL, Zhu Q, Cayabyab F, Low B, He M, Xing S, Vargas F, Yu RT, Atkins A, Liddle C, Ayres J, Raffatellu M, Dorrestein PC, Downes M, Knight R, Evans RM. Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression. Cell Rep 2023; 42:112997. [PMID: 37611587 PMCID: PMC10903535 DOI: 10.1016/j.celrep.2023.112997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/08/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
Colorectal cancer (CRC) is driven by genomic alterations in concert with dietary influences, with the gut microbiome implicated as an effector in disease development and progression. While meta-analyses have provided mechanistic insight into patients with CRC, study heterogeneity has limited causal associations. Using multi-omics studies on genetically controlled cohorts of mice, we identify diet as the major driver of microbial and metabolomic differences, with reductions in α diversity and widespread changes in cecal metabolites seen in high-fat diet (HFD)-fed mice. In addition, non-classic amino acid conjugation of the bile acid cholic acid (AA-CA) increased with HFD. We show that AA-CAs impact intestinal stem cell growth and demonstrate that Ileibacterium valens and Ruminococcus gnavus are able to synthesize these AA-CAs. This multi-omics dataset implicates diet-induced shifts in the microbiome and the metabolome in disease progression and has potential utility in future diagnostic and therapeutic developments.
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Affiliation(s)
- Ting Fu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tao Huan
- Department of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada
| | - Gibraan Rahman
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hui Zhi
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhenjiang Xu
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tae Gyu Oh
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jian Guo
- Department of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada
| | - Sally Coulter
- Storr Liver Centre, Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Anupriya Tripathi
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin L McCarville
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Qiyun Zhu
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fritz Cayabyab
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Brian Low
- Department of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada
| | - Mingxiao He
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shipei Xing
- Department of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada
| | - Fernando Vargas
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruth T Yu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Annette Atkins
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Janelle Ayres
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Manuela Raffatellu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunity, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, USA
| | - Pieter C Dorrestein
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Downes
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ronald M Evans
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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30
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Yue Y, Read TD, Fedirko V, Satten GA, Hu YJ. Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546795. [PMID: 37425938 PMCID: PMC10327031 DOI: 10.1101/2023.06.27.546795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for the objective of testing differential abundance at the genus and community levels while overcoming these difficulties. We demonstrate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than two ad hoc approaches.
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31
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Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci 2023:10.1038/s41593-023-01361-0. [PMID: 37365313 DOI: 10.1038/s41593-023-01361-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed a Bayesian differential ranking algorithm to identify ASD-associated molecular and taxa profiles across 10 cross-sectional microbiome datasets and 15 other datasets, including dietary patterns, metabolomics, cytokine profiles and human brain gene expression profiles. We found a functional architecture along the GBA that correlates with heterogeneity of ASD phenotypes, and it is characterized by ASD-associated amino acid, carbohydrate and lipid profiles predominantly encoded by microbial species in the genera Prevotella, Bifidobacterium, Desulfovibrio and Bacteroides and correlates with brain gene expression changes, restrictive dietary patterns and pro-inflammatory cytokine profiles. The functional architecture revealed in age-matched and sex-matched cohorts is not present in sibling-matched cohorts. We also show a strong association between temporal changes in microbiome composition and ASD phenotypes. In summary, we propose a framework to leverage multi-omic datasets from well-defined cohorts and investigate how the GBA influences ASD.
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Affiliation(s)
- James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dong-Min Jin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | | | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Gibraan Rahman
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julie Carmel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | - Sandra Martin-Brevet
- Laboratory for Research in Neuroimaging, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Berding
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Brittany D Needham
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - María Fernanda Zurita
- Microbiology Institute and Health Science College, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maude David
- Departments of Microbiology & Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Olga V Averina
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Antonio Noto
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
- Microbiome Therapy Center, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ellen Li
- Department of Medicine, Division of Gastroenterology and Hepatology, Stony Brook University, Stony Brook, NY, USA
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Vassilios Fanos
- Neonatal Intensive Care Unit and Neonatal Pathology, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Valery N Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Dennis P Wall
- Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Paúl Cárdenas
- Institute of Microbiology, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Manuel E Baldeón
- Facultad de Ciencias Médicas, de la Salud y la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Sébastien Jacquemont
- Sainte Justine Hospital Research Center, Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Evan Elliott
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Sharon M Donovan
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Bob Carpenter
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Prescient Design, a Genentech Accelerator, New York, NY, USA
| | - Gaspar Taroncher-Oldenburg
- Gaspar Taroncher Consulting, Philadelphia, PA, USA.
- Simons Foundation Autism Research Initiative, Simons Foundation, New York, NY, USA.
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Usyk M, Peters BA, Karthikeyan S, McDonald D, Sollecito CC, Vazquez-Baeza Y, Shaffer JP, Gellman MD, Talavera GA, Daviglus ML, Thyagarajan B, Knight R, Qi Q, Kaplan R, Burk RD. Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies. CELL REPORTS METHODS 2023; 3:100391. [PMID: 36814836 PMCID: PMC9939430 DOI: 10.1016/j.crmeth.2022.100391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/28/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023]
Abstract
In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
| | - Brandilyn A. Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christopher C. Sollecito
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yoshiki Vazquez-Baeza
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Justin P. Shaffer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marc D. Gellman
- Department of Psychology, University of Miami, Miami, FL, USA
| | - Gregory A. Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA, USA
| | - Martha L. Daviglus
- Department of Medicine, University of Illinois-Chicago, Chicago, IL, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Departments of Computer Science and Engineering, and Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert D. Burk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Microbiology & Immunology, and Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
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33
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Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R. Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nat Microbiol 2022; 7:2128-2150. [PMID: 36443458 PMCID: PMC9712116 DOI: 10.1038/s41564-022-01266-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 11/30/2022]
Abstract
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
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Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Asker D Brejnrod
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Holly L Lutz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do, Korea
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jeremiah J Minich
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie M Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yoshiki Vásquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Laxmi Parida
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA
| | | | - Kristen L Beck
- IBM Research, Almaden Research Center, San Jose, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Antonio González
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joshua Ladau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Søren M Karst
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jeff DeReus
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, The University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - James Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
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34
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Abdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice. eLife 2022; 11:e81453. [PMID: 36346385 PMCID: PMC9668333 DOI: 10.7554/elife.81453] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, α-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, although mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces α-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.
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Affiliation(s)
- Reem Abdel-Haq
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Johannes CM Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University West LafayetteWest LafayetteUnited States
| | - Taren Thron
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Mengying Zhang
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - John W Bostick
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Tahmineh Khazaei
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Sujatha Chilakala
- Lawrence J Ellison Institute for Transformative Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Livia H Morais
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Greg Humphrey
- Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical CenterChicagoUnited States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical CenterChicagoUnited States
| | - Jonathan E Katz
- Lawrence J Ellison Institute for Transformative Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Matthew Thomson
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Rob Knight
- Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Department of Computer Science and Engineering, University of California, San DiegoSan DiegoUnited States
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
- Center for Microbiome Innovation, University of California San DiegoSan DiegoUnited States
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University West LafayetteWest LafayetteUnited States
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
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Abstract
Assigning taxonomy remains a challenging topic in microbiome studies, due largely to ambiguity of reads which overlap multiple reference genomes. With the Web of Life (WoL) reference database hosting 10,575 reference genomes and growing, the percentage of ambiguous reads will only increase. The resulting artifacts create both the illusion of co-occurrence and a long tail end of extraneous reference hits that confound interpretation. We introduce genome cover, the fraction of reference genome overlapped by reads, to distinguish these artifacts. We show how to dynamically predict genome cover by read count and examine our model in Staphylococcus aureus monoculture. Our modeling cleanly separates both S. aureus and true contaminants from the false artifacts of reference overlap. We next introduce saturated genome cover, the true fraction of a reference genome overlapped by sample contents. Genome cover may not saturate for low abundance or low prevalence bacteria. We assuage this worry with examination of a large human fecal data set. By compositing the metric across like samples, genome cover saturates even for rare species. We note that it is a threshold on saturated genome cover, not genome cover itself, which indicates a spurious reference hit or distant relative. We present Zebra, a method to compute and threshold the genome cover metric across like samples, a recurrence to estimate genome cover and confirm saturation, and provide guidance for choosing cover thresholds in real world scenarios. Standalone genome cover and integration into Woltka are available: https://github.com/biocore/zebra_filter, https://github.com/qiyunzhu/woltka. IMPORTANCE Taxonomic assignment, assigning sequences to specific taxonomic units, is a crucial processing step in microbiome analyses. Issues in taxonomic assignment affect interpretation of what microbes are present in each sample and may be associated with specific environmental or clinical conditions. Assigning importance to a particular taxon relies strongly on independence of assigned counts. The false inclusion of thousands of correlated taxa makes interpretation ambiguous, leading to underconstrained results which cannot be reproduced. The importance sometimes attached to implausible artifacts such as anthrax or bubonic plague is especially problematic. We show that the Zebra filter retrieves only the nearest relatives of sample contents enabling more reproducible and biologically plausible interpretation of metagenomic data.
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36
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Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell 2022; 185:3789-3806.e17. [PMID: 36179670 PMCID: PMC9567272 DOI: 10.1016/j.cell.2022.09.005] [Citation(s) in RCA: 177] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/13/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts. We report fungal DNA and cells at low abundances across many major human cancers, with differences in community compositions that differ among cancer types, even when accounting for technical background. Fungal histological staining of tissue microarrays supported intratumoral presence and frequent spatial association with cancer cells and macrophages. Comparing intratumoral fungal communities with matched bacteriomes and immunomes revealed co-occurring bi-domain ecologies, often with permissive, rather than competitive, microenvironments and distinct immune responses. Clinically focused assessments suggested prognostic and diagnostic capacities of the tissue and plasma mycobiomes, even in stage I cancers, and synergistic predictive performance with bacteriomes.
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Affiliation(s)
- Lian Narunsky-Haziza
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Micronoma Inc., San Diego, CA, USA
| | - Ilana Livyatan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Guy Amit
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel; Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Antonio González
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Gili Perry
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ruthie Ariel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Arnon Meltser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Justin P Shaffer
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Nora Balint-Lahat
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dadiani
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Einav N Gal-Yam
- Breast Oncology Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Amir Bashan
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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37
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Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R. A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques 2022; 73:34-46. [PMID: 35713407 PMCID: PMC9361692 DOI: 10.2144/btn-2022-0032] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.
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Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carolina S Carpenter
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
- Bioinformatics & Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rodolfo A Salido
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
- InterOme, Inc. Carlsbad, CA 92008, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
- Micronoma Inc. San Diego, CA 92121, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
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