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Xiang Q, Yan X, Shi X, Huang Y, Li L, Zhong J, Xu T, Tang S, Shi W, Zhou K. Prolonged premature rupture of membranes with increased risk of infection is associated with gut accumulation of Pseudomonas from the environment. Comput Struct Biotechnol J 2024; 23:2851-2860. [PMID: 39100803 PMCID: PMC11296040 DOI: 10.1016/j.csbj.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024] Open
Abstract
Background Preterm premature rupture of membranes (PPROM) contributes to over one-third of preterm births, and PPROM infants are more susceptible to infections. However, the risk factors remain poorly understood. We here aim to investigate the association of duration of premature rupture of membranes (PROM) and environmental microbiota with the gut microbiota and infection in PPROM infants. Methods Forty-six premature infants were recruited from two hospitals, and infant fecal and environmental samples were collected. 16 s rRNA sequencing was performed to analyze the fecal and environmental microbiome. Human inflammatory cytokines in cord vein plasma were measured. Results The gut microbiota composition of PPROM infants was different from that of non-PPROM infants, and the microbiome phenotypes were predicted to be associated with a higher risk of infection, further evidenced by the significantly increased levels of IL-6 and IL-8 in cord vein plasma of PPROM infants. The diversity of the gut microbiota in PPROM infants increased significantly as the duration of PROM excessed 12 h, and Pseudomonas contributed significantly to the dynamic changes. The Pseudomonas species in the gut of PPROM infants were highly homologous to those detected in the ward environment, suggesting that prolonged PROM is associated with horizontal transmission of environmental pathogens, leading to a higher risk of infection. Conclusions This study highlights that the duration of PROM is associated with the accumulation of environmental pathogens in the gut of PPROM infants, which is a risk factor for nosocomial infections. Improving environmental hygiene could be effective in optimizing the clinical care of PPROM infants.
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Affiliation(s)
- Quanhang Xiang
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Xudong Yan
- Department of Neonatal Intensive Care Unit, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China
| | - Xing Shi
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yi’e Huang
- Department of Prevention and Healthcare, Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, Shenzhen 518020, China
| | - Lingfeng Li
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Jiacheng Zhong
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Shaohui Tang
- Department of Gastroenterology, the First Affiliated Hospital, Jinan University, Guangzhou 510632, China
| | - Wei Shi
- Department of Obstetrics, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
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2
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Shao Y, Garcia-Mauriño C, Clare S, Dawson NJR, Mu A, Adoum A, Harcourt K, Liu J, Browne HP, Stares MD, Rodger A, Brocklehurst P, Field N, Lawley TD. Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. Nat Microbiol 2024; 9:2570-2582. [PMID: 39242817 DOI: 10.1038/s41564-024-01804-9] [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: 04/22/2024] [Accepted: 08/05/2024] [Indexed: 09/09/2024]
Abstract
Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.
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Affiliation(s)
- Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| | | | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas J R Dawson
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Anne Adoum
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Katherine Harcourt
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Junyan Liu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Alison Rodger
- Institute for Global Health, University College London, London, UK
| | - Peter Brocklehurst
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Nigel Field
- Institute for Global Health, University College London, London, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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3
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Cheng M, Xu Y, Cui X, Wei X, Chang Y, Xu J, Lei C, Xue L, Zheng Y, Wang Z, Huang L, Zheng M, Luo H, Leng Y, Jiang C. Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness. Nat Commun 2024; 15:8361. [PMID: 39333527 PMCID: PMC11436904 DOI: 10.1038/s41467-024-52713-8] [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: 02/14/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.
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Affiliation(s)
- Minghui Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yingjie Xu
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Xiao Cui
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
| | - Yundi Chang
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Jun Xu
- Department of Critical Care Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Lei Xue
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Yifan Zheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
| | - Zhang Wang
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Lingtong Huang
- Department of Critical Care Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Yuxin Leng
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China.
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China.
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4
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Pu L, Shamir R. 4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs. Nucleic Acids Res 2024:gkae799. [PMID: 39287139 DOI: 10.1093/nar/gkae799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/13/2024] [Accepted: 09/02/2024] [Indexed: 09/19/2024] Open
Abstract
Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.
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Affiliation(s)
- Lianrong Pu
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- School of Computer Science and Technology, Shandong University, Qingdao, China
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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5
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Thänert R, Schwartz DJ, Keen EC, Hall-Moore C, Wang B, Shaikh N, Ning J, Rouggly-Nickless LC, Thänert A, Ferreiro A, Fishbein SRS, Sullivan JE, Radmacher P, Escobedo M, Warner BB, Tarr PI, Dantas G. Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants. Cell Host Microbe 2024:S1931-3128(24)00286-5. [PMID: 39197454 DOI: 10.1016/j.chom.2024.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/24/2024] [Accepted: 07/31/2024] [Indexed: 09/01/2024]
Abstract
Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.
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Affiliation(s)
- Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Drew J Schwartz
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Women's Infectious Diseases Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric C Keen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jie Ning
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Anna Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aura Ferreiro
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janice E Sullivan
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children's Hospital, Louisville, KY 40202, USA
| | - Paula Radmacher
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children's Hospital, Louisville, KY 40202, USA
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma, Oklahoma City, OK 73104, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
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6
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Chibwe K, Sundararaju S, Zhang L, Tsui C, Tang P, Ling F. Intra-hospital microbiome variability is driven by accessibility and clinical activities. Microbiol Spectr 2024; 12:e0029624. [PMID: 38940596 PMCID: PMC11302010 DOI: 10.1128/spectrum.00296-24] [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: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024] Open
Abstract
The hospital environmental microbiome, which can affect patients' and healthcare workers' health, is highly variable and the drivers of this variability are not well understood. In this study, we collected 37 surface samples from the neonatal intensive care unit (NICU) in an inpatient hospital before and after the operation began. Additionally, healthcare workers collected 160 surface samples from five additional areas of the hospital. All samples were analyzed using 16S rRNA gene amplicon sequencing, and the samples collected by healthcare workers were cultured. The NICU samples exhibited similar alpha and beta diversities before and after opening, which indicated that the microbiome there was stable over time. Conversely, the diversities of samples taken after opening varied widely by area. Principal coordinate analysis (PCoA) showed the samples clustered into two distinct groups: high alpha diversity [the pediatric intensive care unit (PICU), pathology lab, and microbiology lab] and low alpha diversity [the NICU, pediatric surgery ward, and infection prevention and control (IPAC) office]. Least absolute shrinkage and selection operator (LASSO) classification models identified 156 informative amplicon sequence variants (ASVs) for predicting the sample's area of origin. The testing accuracy ranged from 86.37% to 100%, which outperformed linear and radial support vector machine (SVM) and random forest models. ASVs of genera that contain emerging pathogens were identified in these models. Culture experiments had identified viable species among the samples, including potential antibiotic-resistant bacteria. Though area type differences were not noted in the culture data, the prevalences and relative abundances of genera detected positively correlated with 16S sequencing data. This study brings to light the microbial community temporal and spatial variation within the hospital and the importance of pathogenic and commensal bacteria to understanding dispersal patterns for infection control. IMPORTANCE We sampled surface samples from a newly built inpatient hospital in multiple areas, including areas accessed by only healthcare workers. Our analysis of the neonatal intensive care unit (NICU) showed that the microbiome was stable before and after the operation began, possibly due to access restrictions. Of the high-touch samples taken after opening, areas with high diversity had more potential external seeds (long-term patients and clinical samples), and areas with low diversity and had fewer (short-term or newborn patients). Classification models performed at high accuracy and identified biomarkers that could be used for more targeted surveillance and infection control. Though culturing data yielded viability and antibiotic-resistance information, it disproportionately detected the presence of genera relative to 16S data. This difference reinforces the utility of 16S sequencing in profiling hospital microbiomes. By examining the microbiome over time and in multiple areas, we identified potential drivers of the microbial variation within a hospital.
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Affiliation(s)
- Kaseba Chibwe
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Lin Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Clement Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Singapore
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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7
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Gilbert JA, Hartmann EM. The indoors microbiome and human health. Nat Rev Microbiol 2024:10.1038/s41579-024-01077-3. [PMID: 39030408 DOI: 10.1038/s41579-024-01077-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/21/2024]
Abstract
Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.
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Affiliation(s)
- Jack A Gilbert
- Department of Paediatrics, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
- Department of Medicine, Division of Pulmonary Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
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8
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Wolska M, Wypych TP, Rodríguez-Viso P. The Influence of Premature Birth on the Development of Pulmonary Diseases: Focus on the Microbiome. Metabolites 2024; 14:382. [PMID: 39057705 PMCID: PMC11279213 DOI: 10.3390/metabo14070382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Globally, around 11% of neonates are born prematurely, comprising a highly vulnerable population with a myriad of health problems. Premature births are often accompanied by an underdeveloped immune system biased towards a Th2 phenotype and microbiota dysbiosis. Typically, a healthy gut microbiota interacts with the host, driving the proper maturation of the host immunity. However, factors like cesarean section, formula milk feeding, hospitalization in neonatal intensive care units (NICU), and routine antibiotic treatments compromise microbial colonization and increase the risk of developing related diseases. This, along with alterations in the innate immune system, could predispose the neonates to the development of respiratory diseases later in life. Currently, therapeutic strategies are mainly focused on restoring gut microbiota composition using probiotics and prebiotics. Understanding the interactions between the gut microbiota and the immature immune system in premature neonates could help to develop novel therapeutic strategies for treating or preventing gut-lung axis disorders.
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Affiliation(s)
| | - Tomasz Piotr Wypych
- Laboratory of Host-Microbiota Interactions, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Ludwika Pasteura 3, 02-093 Warsaw, Poland; (M.W.); (P.R.-V.)
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9
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Klimov PB, Hubert J, Erban T, Alejandra Perotti M, Braig HR, Flynt A, He Q, Cui Y. Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q). Int J Parasitol 2024:S0020-7519(24)00138-3. [PMID: 38992783 DOI: 10.1016/j.ijpara.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.
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Affiliation(s)
- Pavel B Klimov
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA; Tyumen State University, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen, Russia.
| | - Jan Hubert
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia; Czech University of Life Science, Faculty of Microbiology Nutrient and Dietics, Prague, Czechia
| | - Tomas Erban
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia
| | - M Alejandra Perotti
- University of Reading, Ecology and Evolutionary Biology Section, School of Biological Sciences, Reading RG6 6AS, United Kingdom
| | - Henk R Braig
- Institute and Museum of Natural Sciences, Faculty of Natural and Exact Sciences, National University of San Juan, San Juan, J5400 DNQ, Argentina
| | - Alex Flynt
- University of Southern Mississippi, School of Biological, Environmental, and Earth Sciences, Hattiesburg, MS, USA
| | - Qixin He
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA.
| | - Yubao Cui
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University.Wuxi, PR Chin.
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10
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [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: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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11
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Wang W, Qiu Z, Li H, Wu X, Cui Y, Xie L, Chang B, Li P, Zeng H, Ding T. Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171703. [PMID: 38490424 DOI: 10.1016/j.scitotenv.2024.171703] [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: 10/16/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Healthcare-associated infections (HAIs) pose significant risks to pediatric patients in outpatient settings. To prevent HAIs, understanding the sources and transmission routes of pathogenic microorganisms is crucial. This study aimed to identify the sources of opportunistic bacterial pathogens (OBPs) in pediatric outpatient settings and determine their transmission routes. Furthermore, assessing the public health risks associated with the core OBPs is important. We collected 310 samples from various sites in pediatric outpatient areas and quantified the bacteria using qPCR and CFU counting. We also performed 16S rRNA gene and single-bacterial whole-genome sequencing to profile the transmission routes and antibiotic resistance characteristics of OBPs. We observed significant variations in microbial diversity and composition among sampling sites in pediatric outpatient settings, with active communication of the microbiota between linked areas. We found that the primary source of OBPs in multi-person contact areas was the hand surface, particularly in pediatric patients. Five core OBPs, Staphylococcus epidermidis, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus mitis, and Streptococcus oralis, were mainly derived from pediatric patients and spread into the environment. These OBPs accumulated at multi-person contact sites, resulting in high microbial diversity in these areas. Transmission tests confirmed the challenging spread of these pathogens, with S. epidermidis transferring from the patient's hand to the environment, leading to an increased abundance and emergence of related strains. More importantly, S. epidermidis isolated from pediatric patients carried more antibiotic-resistance genes. In addition, two strains of multidrug-resistant A. baumannii were isolated from both a child and a parent, confirming the transmission of the five core OBPs centered around pediatric patients and multi-person contact areas. Our results demonstrate that pediatric patients serve as a significant source of OBPs in pediatric outpatient settings. OBPs carried by pediatric patients pose a high public health risk. To effectively control HAIs, increasing hand hygiene measures in pediatric patients and enhancing the frequency of disinfection in multi-person contact areas remains crucial. By targeting these preventive measures, the spread of OBPs can be reduced, thereby mitigating the risk of HAIs in pediatric outpatient settings.
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Affiliation(s)
- Wan Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Zongyao Qiu
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China
| | - Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Lixiang Xie
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Peipei Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China.
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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12
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Younge N. Influence of infant microbiome on health and development. Clin Exp Pediatr 2024; 67:224-231. [PMID: 37605538 PMCID: PMC11065641 DOI: 10.3345/cep.2023.00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/08/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023] Open
Abstract
The microbiome is a complex ecosystem comprising microbes, their genomes, and the surrounding environment. The microbiome plays a critical role in early human development, including maturation of the host immune system and gastrointestinal tract. Multiple factors, including diet, anti-biotic use, and other environmental exposures, influence the establishment of the microbiome during infancy. Numerous studies have identified associations between the microbiome and neonatal diseases, including necrotizing enterocolitis, sepsis, and malnutrition. Furthermore, there is compelling evidence that perturbation of the microbiome in early life can have lasting developmental effects that increase an individual's risk for immune and metabolic diseases in later life. Supplementation of the microbiome with probiotics reduces the risk of necrotizing enterocolitis and sepsis in at-risk infants. This review focuses on the structure and function of the infant microbiome, the environmental and clinical factors that influence its assembly, and its impact on infant health and development.
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13
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Wei X, Tsai MS, Liang L, Jiang L, Hung CJ, Jelliffe-Pawlowski L, Rand L, Snyder M, Jiang C. Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process. Cell Rep 2024; 43:114078. [PMID: 38598334 DOI: 10.1016/j.celrep.2024.114078] [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: 09/15/2023] [Revised: 03/01/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.
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Affiliation(s)
- Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ming-Shian Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liang Liang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liuyiqi Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Chia-Jui Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
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14
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Yang R, Wang Y, Ying Z, Shi Z, Song Y, Yan J, Hou S, Zhao Z, Hu Y, Chen Q, Peng W, Li X. Inspecting mother-to-infant microbiota transmission: disturbance of strain inheritance by cesarian section. Front Microbiol 2024; 15:1292377. [PMID: 38486699 PMCID: PMC10937581 DOI: 10.3389/fmicb.2024.1292377] [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: 09/11/2023] [Accepted: 02/16/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction The initial acquisition and subsequent development of the microbiota in early life is crucial to future health. Cesarean-section (CS) birth is considered to affect early microbial transmission from mother to infant. Methods In this study, we collected fecal samples from 34 CS infants and their mothers from West China Second Hospital, Sichuan University to assess the microbiota developmental trajectory of mothers and infants. We explored mother-infant gut microbiome transmission via comparison with corresponding Finnish data. Results Metagenomic analysis of gut microbiota profiles indicated that the communities of mothers and infants were distinct. The composition of the infant gut microbiome was highly variable but also followed predictable patterns in the early stages of life. Maternal communities were stable and mainly dominated by species from Bacteroidacea spp. We used PStrain to analyze and visualize strain transmission in each mother-infant pair. Excluding missing data, we included 32 mother-infant pairs for analysis of strain transmission. Most CS deliveries (65.6%, 21/32) did not demonstrate transmission of strains from mother to infant. To further explore the mother-infant strain transmission, we analyzed metagenomics data from Finnish mother-infant pairs. A total of 32 mother-infant pairs were included in the analysis, including 28 vaginal delivery (VD) infants and four CS infants. Strain transmission was observed in 30 infants, including 28 VD infants and two CS infants. All VD infants received transmitted stains from their mothers. Finally, a total of 193 strain transmission events were observed, comprising 131 strains and 45 species. Discussion Taken together, our data suggested that delivery mode was an important factor influencing the mother-infant strain transmission.
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Affiliation(s)
- Ru Yang
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yinan Wang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhiye Ying
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Sichuan, China
- Medical Big Data Center, Sichuan University, Chengdu, Sichuan, China
| | - Zeyao Shi
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yan Song
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Jing Yan
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Shulin Hou
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Zicheng Zhao
- Shenzhen Byoryn Technology, Shenzhen, Guangdong, China
| | - Yanling Hu
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Qiong Chen
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Wentao Peng
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Xiaowen Li
- Department of Neonatology Nursing, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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15
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Zhang L, Agrawal M, Ng SC, Jess T. Early-life exposures and the microbiome: implications for IBD prevention. Gut 2024; 73:541-549. [PMID: 38123972 PMCID: PMC11150004 DOI: 10.1136/gutjnl-2023-330002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
The early-life period is one of microbiome establishment and immune maturation. Early-life exposures are increasingly being recognised to play an important role in IBD risk. The composition of functions of the gut microbiome in the prenatal, perinatal, and postnatal period may be crucial towards development of health or disease, including IBD, later in life. We herein present a comprehensive summary of the interplay between early-life factors and microbiome perturbations, and their association with risk of IBD. In addition, we provide an overview of host and external factors in early life that are known to impact gut microbiome maturation and exposures implicated in IBD risk. Considering the emerging concept of IBD prevention, we propose strategies to minimise maternal and offspring exposure to potentially harmful variables and recommend protective measures during pregnancy and the postpartum period. This holistic view of early-life factors and microbiome signatures among mothers and their offspring will help frame our current understanding of their importance towards IBD pathogenesis and frame the roadmap for preventive strategies.
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Affiliation(s)
- Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Manasi Agrawal
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York NY, New York, USA
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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16
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VanOrmer M, Thompson M, Thoene M, Riethoven JJ, Natarajan SK, Hanson C, Anderson-Berry A. The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study. PLoS One 2024; 19:e0297558. [PMID: 38381745 PMCID: PMC10880995 DOI: 10.1371/journal.pone.0297558] [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: 07/07/2023] [Accepted: 01/08/2024] [Indexed: 02/23/2024] Open
Abstract
OBJECTIVE The gastrointestinal microbiome in preterm infants exhibits significant influence on optimal outcomes-with dysbiosis shown to substantially increase the risk of the life-threatening necrotizing enterocolitis. Iron is a vital nutrient especially during the perinatal window of rapid hemoglobin production, tissue growth, and foundational neurodevelopment. However, excess colonic iron exhibits potent oxidation capacity and alters the gut microbiome-potentially facilitating the proliferation of pathological bacterial strains. Breastfed preterm infants routinely receive iron supplementation starting 14 days after delivery and are highly vulnerable to morbidities associated with gastrointestinal dysbiosis. Therefore, we set out to determine if routine iron supplementation alters the preterm gut microbiome. METHODS After IRB approval, we collected stool specimens from 14 infants born <34 weeks gestation in the first, second, and fourth week of life to assess gut microbiome composition via 16S rRNA sequencing. RESULTS We observed no significant differences in either phyla or key genera relative abundance between pre- and post-iron timepoints. We observed notable shifts in infant microbiome composition based on season of delivery. CONCLUSION Though no obvious indication of iron-induced dysbiosis was observed in this unique study in the setting of prematurity, further investigation in a larger sample is warranted to fully understand iron's impact on the gastrointestinal milieu.
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Affiliation(s)
- Matthew VanOrmer
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Maranda Thompson
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Melissa Thoene
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Jean-Jack Riethoven
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Sathish Kumar Natarajan
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Corrine Hanson
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Ann Anderson-Berry
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, United States of America
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17
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Turroni F, van Sinderen D, Ventura M. The infant gut microbiota as the cornerstone for future gastrointestinal health. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:93-119. [PMID: 38637108 DOI: 10.1016/bs.aambs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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Allert M, Ferretti P, Johnson KE, Heisel T, Gonia S, Knights D, Fields DA, Albert FW, Demerath EW, Gale CA, Blekhman R. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother's milk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.28.577594. [PMID: 38328166 PMCID: PMC10849666 DOI: 10.1101/2024.01.28.577594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular by B. longum. Infant stool samples dominated by B. longum also showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated with de-novo molecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother's milk and their infant's gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.
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Affiliation(s)
- Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Pamela Ferretti
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Sara Gonia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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19
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Yew WC, Young GR, Nelson A, Cheung W, Stewart CJ, Bridge SH, Granger C, Berrington JE, Embleton ND, Smith DL. The core phageome and its interrelationship with preterm human milk lipids. Cell Rep 2023; 42:113373. [PMID: 37967008 DOI: 10.1016/j.celrep.2023.113373] [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: 03/24/2023] [Revised: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023] Open
Abstract
Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite this, interrelationships between lipids and phages are poorly characterized in preterm HM. Shotgun metagenomics and untargeted lipidomics of phage and lipid profiles from 99 preterm HM samples reveals that phages are abundant and prevalent from the first week and throughout the first 100 days of lactation. Phage-host richness of preterm HM increases longitudinally. Core phage communities characterized by Staphylococcus- and Propionibacterium-infecting phages are significantly correlated with long-chain fatty acid abundances over lactational age. We report here a phage-lipid interaction in preterm HM, highlighting the potential importance of phage carriage in preterm HM. These results reveal possible strategies for phage carriage in HM and their importance in early-life microbiota development.
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Affiliation(s)
- Wen C Yew
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gregory R Young
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Simon H Bridge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Claire Granger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Neonatal Medicine, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Janet E Berrington
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Neonatal Medicine, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Nicholas D Embleton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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20
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Gimenes de Castro B, Mari Fredi B, Dos Santos Bezerra R, Alcantara QA, Milani Neme CE, Mascarelli DE, Carvalho Tahyra AS, Dos-Santos D, Nappi CR, Santos de Oliveira F, Pereira Freire F, Ballestero G, Menuci Lima JB, de Andrade Bolsoni J, Lourenço Gebenlian J, Lopes Bibo N, Soares Silva N, de Carvalho Santos N, Simionatto Zucherato V, Chagas Peronni K, Guariz Pinheiro D, Dias-Neto E, Gambero Gaspar G, Roberto Bollela V, da Silva Silveira V, Maria Fontes A, Maria Martinez-Rossi N, Nanev Slavov S, Paulo Bianchi Ximenez J, Barbosa F, Araújo Silva W. Metabarcoding approach to identify bacterial community profiling related to nosocomial infection and bacterial trafficking-routes in hospital environments. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2023; 86:803-815. [PMID: 37565650 DOI: 10.1080/15287394.2023.2243978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Nosocomial infections (NIs) appear in patients under medical care in the hospital. The surveillance of the bacterial communities employing high-resolution 16S rRNA profiling, known as metabarcoding, represents a reliable method to establish factors that may influence the composition of the bacterial population during NIs. The present study aimed to utilize high-resolution 16S rRNA profiling to identify high bacterial diversity by analyzing 11 inside and 10 outside environments from the General Hospital of Ribeirão Preto Medical School, Brazil. Our results identified a high bacterial diversity, and among these, the most abundant bacterial genera linked to NIs were Cutibacterium, Streptococcus, Staphylococcus, and Corynebacterium. A Acinetobacter was detected in cafeterias, bus stops, and adult and pediatric intensive care units (ICUs). Data suggest an association between transport and alimentation areas proximal to the hospital ICU environment. Interestingly, the correlation and clusterization analysis showed the potential of the external areas to directly influence the ICU pediatric department microbial community, including the outpatient's clinic, visitor halls, patient reception, and the closest cafeterias. Our results demonstrate that high-resolution 16S rRNA profiling is a robust and reliable tool for bacterial genomic surveillance. In addition, the metabarcoding approach might help elaborate decontamination policies, and consequently reduce NIs.
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Affiliation(s)
| | - Bruno Mari Fredi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafael Dos Santos Bezerra
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center, General Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Queren Apuque Alcantara
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics, General Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | | | - Douglas Dos-Santos
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Camilla Rizzo Nappi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Giulia Ballestero
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | | | - Naira Lopes Bibo
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | | | - Kamila Chagas Peronni
- Department of the Research and Innovation, Institute for Cancer Research, Guarapuava, Parana, Brazil
| | - Daniel Guariz Pinheiro
- Department of Technology, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, International Research Center, A.C. Camargo Cancer Center, Jaboticabal, São Paulo, Brazil
| | - Gilberto Gambero Gaspar
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Valdes Roberto Bollela
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Vanessa da Silva Silveira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Aparecida Maria Fontes
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nilce Maria Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Svetoslav Nanev Slavov
- Regional Blood Center, General Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - João Paulo Bianchi Ximenez
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Wilson Araújo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center, General Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Department of the Research and Innovation, Institute for Cancer Research, Guarapuava, Parana, Brazil
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21
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Beharry KD, Latkowska M, Valencia AM, Allana A, Soto J, Cai CL, Golombek S, Hand I, Aranda JV. Factors Influencing Neonatal Gut Microbiome and Health with a Focus on Necrotizing Enterocolitis. Microorganisms 2023; 11:2528. [PMID: 37894186 PMCID: PMC10608807 DOI: 10.3390/microorganisms11102528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/21/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Maturational changes in the gut start in utero and rapidly progress after birth, with some functions becoming fully developed several months or years post birth including the acquisition of a full gut microbiome, which is made up of trillions of bacteria of thousands of species. Many factors influence the normal development of the neonatal and infantile microbiome, resulting in dysbiosis, which is associated with various interventions used for neonatal morbidities and survival. Extremely low gestational age neonates (<28 weeks' gestation) frequently experience recurring arterial oxygen desaturations, or apneas, during the first few weeks of life. Apnea, or the cessation of breathing lasting 15-20 s or more, occurs due to immature respiratory control and is commonly associated with intermittent hypoxia (IH). Chronic IH induces oxygen radical diseases of the neonate, including necrotizing enterocolitis (NEC), the most common and devastating gastrointestinal disease in preterm infants. NEC is associated with an immature intestinal structure and function and involves dysbiosis of the gut microbiome, inflammation, and necrosis of the intestinal mucosal layer. This review describes the factors that influence the neonatal gut microbiome and dysbiosis, which predispose preterm infants to NEC. Current and future management and therapies, including the avoidance of dysbiosis, the use of a human milk diet, probiotics, prebiotics, synbiotics, restricted antibiotics, and fecal transplantation, for the prevention of NEC and the promotion of a healthy gut microbiome are also reviewed. Interventions directed at boosting endogenous and/or exogenous antioxidant supplementation may not only help with prevention, but may also lessen the severity or shorten the course of the disease.
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Affiliation(s)
- Kay D. Beharry
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (M.L.); (C.L.C.); (S.G.); (J.V.A.)
| | - Magdalena Latkowska
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (M.L.); (C.L.C.); (S.G.); (J.V.A.)
| | - Arwin M. Valencia
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Saddleback Memorial Medical Center, Laguna Hills, CA 92653, USA;
| | - Ahreen Allana
- Department of Pediatrics, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (A.A.); (J.S.)
| | - Jatnna Soto
- Department of Pediatrics, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (A.A.); (J.S.)
| | - Charles L. Cai
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (M.L.); (C.L.C.); (S.G.); (J.V.A.)
| | - Sergio Golombek
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (M.L.); (C.L.C.); (S.G.); (J.V.A.)
| | - Ivan Hand
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Kings County Hospital Center, Brooklyn, NY 11203, USA;
| | - Jacob V. Aranda
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (M.L.); (C.L.C.); (S.G.); (J.V.A.)
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22
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Young GR, Nelson A, Stewart CJ, Smith DL. Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease. Curr Opin Microbiol 2023; 75:102379. [PMID: 37647765 DOI: 10.1016/j.mib.2023.102379] [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: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Abstract
Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.
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Affiliation(s)
- Gregory R Young
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Andrew Nelson
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | | | - Darren L Smith
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK.
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23
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Young GR, Sherry A, Smith DL. Built environment microbiomes transition from outdoor to human-associated communities after construction and commissioning. Sci Rep 2023; 13:15854. [PMID: 37740013 PMCID: PMC10516947 DOI: 10.1038/s41598-023-42427-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023] Open
Abstract
The microbiota of the built environment is linked to usage, materials and, perhaps most importantly, human health. Many studies have attempted to identify ways of modulating microbial communities within built environments to promote health. None have explored how these complex communities assemble initially, following construction of new built environments. This study used high-throughput targeted sequencing approaches to explore bacterial community acquisition and development throughout the construction of a new build. Microbial sampling spanned from site identification, through the construction process to commissioning and use. Following commissioning of the building, bacterial richness and diversity were significantly reduced (P < 0.001) and community structure was altered (R2 = 0.14; P = 0.001). Greater longitudinal community stability was observed in outdoor environments than indoor environments. Community flux in indoor environments was associated with human interventions driving environmental selection, which increased 10.4% in indoor environments following commissioning. Increased environmental selection coincided with a 12% reduction in outdoor community influence on indoor microbiomes (P = 2.00 × 10-15). Indoor communities became significantly enriched with human associated genera including Escherichia, Pseudomonas, and Klebsiella spp. These data represent the first to characterize the initial assembly of bacterial communities in built environments and will inform future studies aiming to modulate built environment microbiota.
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Affiliation(s)
- Gregory R Young
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, NE1 8ST, UK
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, NE1 8ST, UK
| | - Angela Sherry
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, NE1 8ST, UK
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, NE1 8ST, UK
| | - Darren L Smith
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, NE1 8ST, UK.
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, NE1 8ST, UK.
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24
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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25
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Diorio-Toth L, Wallace MA, Farnsworth CW, Wang B, Gul D, Kwon JH, Andleeb S, Burnham CAD, Dantas G. Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids. mSystems 2023; 8:e0020623. [PMID: 37439570 PMCID: PMC10469867 DOI: 10.1128/msystems.00206-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/02/2023] [Indexed: 07/14/2023] Open
Abstract
Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive care unit sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. Using culture-based methods, we recovered 822 bacterial isolates representing 104 unique species and genomospecies. Genomic analyses revealed long-term colonization by Pseudomonas spp. and Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples of long-term persistence of resistance-conferring plasmids in unrelated hosts. These data indicate that antibiotic resistance (AR) in Pseudomonas spp. is maintained both by strain colonization and horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter spp. and Enterobacterales, independent of colonization. These results emphasize the importance of proactive, genomic-focused surveillance of built environments to mitigate MDRO spread. IMPORTANCE Hospital sinks are frequently linked to outbreaks of antibiotic-resistant bacteria. Here, we used whole-genome sequencing to track the long-term colonization patterns in intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. We analyzed 822 bacterial genomes, representing over 100 different species. We identified long-term contamination by opportunistic pathogens, as well as transient appearance of other common pathogens. We found that bacteria recovered from the ICU had more antibiotic resistance genes (ARGs) in their genomes compared to matched community spaces. We also found that many of these ARGs are harbored on mobilizable plasmids, which were found shared in the genomes of unrelated bacteria. Overall, this study provides an in-depth view of contamination patterns for common nosocomial pathogens and identifies specific targets for surveillance.
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Affiliation(s)
- Luke Diorio-Toth
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Danish Gul
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Jennie H. Kwon
- Department of Medicine, Washington University School of Medicine in St Louis, St. Louis, Missouri, USA
| | - Saadia Andleeb
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, Missouri, USA
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26
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Rosenboom I, Pust MM, Pirr S, Bakker A, Willers M, Davenport CF, Wiehlmann L, Viemann D, Tümmler B. Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life. ISME COMMUNICATIONS 2023; 3:75. [PMID: 37474785 PMCID: PMC10359316 DOI: 10.1038/s43705-023-00285-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of the above-mentioned factors on the premature-born infants' respiratory metagenome or more generally its maturation is unknown. We therefore applied shotgun metagenome sequencing of oropharyngeal swabs to analyze the airway metagenome development of 24 preterm infants from one week postpartum to 15 months of age. Beta diversity analysis revealed a distinct clustering of airway microbial communities from hospitalized preterms and samples after hospital discharge. At nine and 15 months of age, the preterm infants lost their hospital-acquired individual metagenome signatures towards a common taxonomic structure. However, ecological network analysis and Random Forest classification of cross-sectional data revealed that by this age the preterm infants did not succeed in establishing the uniform and stable bacterial community structures that are characteristic for healthy full-term infants.
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Affiliation(s)
- Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Pirr
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Alina Bakker
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Maike Willers
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Dorothee Viemann
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Translational Pediatrics, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Center for Infection Research, University Würzburg, Würzburg, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.
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27
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Mirhakkak MH, Chen X, Ni Y, Heinekamp T, Sae-Ong T, Xu LL, Kurzai O, Barber AE, Brakhage AA, Boutin S, Schäuble S, Panagiotou G. Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome. Nat Commun 2023; 14:4369. [PMID: 37474497 PMCID: PMC10359302 DOI: 10.1038/s41467-023-39982-5] [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: 06/27/2022] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Abstract
Aspergillus fumigatus, an opportunistic human pathogen, frequently infects the lungs of people with cystic fibrosis and is one of the most common causes of infectious-disease death in immunocompromised patients. Here, we construct 252 strain-specific, genome-scale metabolic models of this important fungal pathogen to study and better understand the metabolic component of its pathogenic versatility. The models show that 23.1% of A. fumigatus metabolic reactions are not conserved across strains and are mainly associated with amino acid, nucleotide, and nitrogen metabolism. Profiles of non-conserved reactions and growth-supporting reaction fluxes are sufficient to differentiate strains, for example by environmental or clinical origin. In addition, shotgun metagenomics analysis of sputum from 40 cystic fibrosis patients (15 females, 25 males) before and after diagnosis with an A. fumigatus colonization suggests that the fungus shapes the lung microbiome towards a more beneficial fungal growth environment associated with aromatic amino acid availability and the shikimate pathway. Our findings are starting points for the development of drugs or microbiome intervention strategies targeting fungal metabolic needs for survival and colonization in the non-native environment of the human lung.
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Affiliation(s)
- Mohammad H Mirhakkak
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Xiuqiang Chen
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Yueqiong Ni
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Tongta Sae-Ong
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Lin-Lin Xu
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, 97080, Würzburg, Germany
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
- National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich-Schiller-University Jena, 07745, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07745, Jena, Germany
| | - Sebastien Boutin
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23562, Lübeck, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, 69120, Heidelberg, Germany
| | - Sascha Schäuble
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany.
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.
- Friedrich Schiller University, Faculty of Biological Sciences, Jena, 07745, Germany.
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28
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Lopez-Santamarina A, Mondragon ADC, Cardelle-Cobas A, Santos EM, Porto-Arias JJ, Cepeda A, Miranda JM. Effects of Unconventional Work and Shift Work on the Human Gut Microbiota and the Potential of Probiotics to Restore Dysbiosis. Nutrients 2023; 15:3070. [PMID: 37447396 DOI: 10.3390/nu15133070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
The work environment is a factor that can significantly influence the composition and functionality of the gut microbiota of workers, in many cases leading to gut dysbiosis that will result in serious health problems. The aim of this paper was to provide a compilation of the different studies that have examined the influence of jobs with unconventional work schedules and environments on the gut microbiota of workers performing such work. As a possible solution, probiotic supplements, via modulation of the gut microbiota, can moderate the effects of sleep disturbance on the immune system, as well as restore the dysbiosis produced. Rotating shift work has been found to be associated with an increase in the risk of various metabolic diseases, such as obesity, metabolic syndrome, and type 2 diabetes. Sleep disturbance or lack of sleep due to night work is also associated with metabolic diseases. In addition, sleep disturbance induces a stress response, both physiologically and psychologically, and disrupts the healthy functioning of the gut microbiota, thus triggering an inflammatory state. Other workers, including military, healthcare, or metallurgy workers, as well as livestock farmers or long-travel seamen, work in environments and schedules that can significantly affect their gut microbiota.
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Affiliation(s)
- Aroa Lopez-Santamarina
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alicia Del Carmen Mondragon
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Eva Maria Santos
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo km. 4.5, Pachuca 42076, Hidalgo, Mexico
| | - Jose Julio Porto-Arias
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alberto Cepeda
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Jose Manuel Miranda
- Laboratorio de Higiene Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
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Snyder KB, Hunter CJ. Bugs and the barrier: A review of the gut microbiome and intestinal barrier in necrotizing enterocolitis. Semin Pediatr Surg 2023; 32:151310. [PMID: 37290337 DOI: 10.1016/j.sempedsurg.2023.151310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease that affects premature neonates. It frequently results in significant morbidity and mortality for those affected. Years of research into the pathophysiology of NEC have revealed it to be a variable and multifactorial disease. However, there are risk factors associated with NEC including low birth weight, prematurity, intestinal immaturity, alterations in microbial colonization, and history of rapid or formula based enteral feeds (Fig. 1).1-3 An accepted generalization of the pathogenesis of NEC includes a hyperresponsive immune reaction to insults such as ischemia, starting formula feeds, or alterations in the microbiome with pathologic bacterial colonization and translocation. This reaction causes a hyperinflammatory response disrupting the normal intestinal barrier, allowing abnormal bacterial translocation and ultimately sepsis.1,2,4 This review will focus specifically on the interactions with the microbiome and intestinal barrier function in NEC.
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Affiliation(s)
- K Brooke Snyder
- Division of Pediatric Surgery, Oklahoma Children's Hospital, 1200 Everett Drive, ET NP 2320 Oklahoma City, OK 73104, United States; The University of Oklahoma Health Sciences Center, Department of Surgery, 800 Research Parkway, Suite 449, Oklahoma City, OK 73104, United States
| | - Catherine J Hunter
- Division of Pediatric Surgery, Oklahoma Children's Hospital, 1200 Everett Drive, ET NP 2320 Oklahoma City, OK 73104, United States; The University of Oklahoma Health Sciences Center, Department of Surgery, 800 Research Parkway, Suite 449, Oklahoma City, OK 73104, United States.
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Manara S, Selma-Royo M, Huang KD, Asnicar F, Armanini F, Blanco-Miguez A, Cumbo F, Golzato D, Manghi P, Pinto F, Valles-Colomer M, Amoroso L, Corrias MV, Ponzoni M, Raffaetà R, Cabrera-Rubio R, Olcina M, Pasolli E, Collado MC, Segata N. Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. Curr Biol 2023; 33:1939-1950.e4. [PMID: 37116481 PMCID: PMC10234599 DOI: 10.1016/j.cub.2023.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/28/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.
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Affiliation(s)
- Serena Manara
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Marta Selma-Royo
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy; Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Kun D Huang
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Francesco Asnicar
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Federica Armanini
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Aitor Blanco-Miguez
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Fabio Cumbo
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Davide Golzato
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Paolo Manghi
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Federica Pinto
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Mireia Valles-Colomer
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Loredana Amoroso
- Oncology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Roberta Raffaetà
- Ca' Foscari University Venice, Department of Philosophy and Cultural Heritage and NICHE, Malcanton Marcorà, Dorsoduro 3484/D, 30123 Venice, Italy
| | - Raul Cabrera-Rubio
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Mari Olcina
- Department of Preventive Medicine and Public Health, Faculty of Pharmacy, Universitat de València, Av. Vicent Andrés Estellés s/n, Burjassot, Valencia 46100, Spain
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Naples, Italy.
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain.
| | - Nicola Segata
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy.
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Fung DLX, Li X, Leung CK, Hu P. A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data. BIOINFORMATICS ADVANCES 2023; 3:vbad059. [PMID: 37228387 PMCID: PMC10203376 DOI: 10.1093/bioadv/vbad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/03/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023]
Abstract
Motivation Human microbiome is complex and highly dynamic in nature. Dynamic patterns of the microbiome can capture more information than single point inference as it contains the temporal changes information. However, dynamic information of the human microbiome can be hard to be captured due to the complexity of obtaining the longitudinal data with a large volume of missing data that in conjunction with heterogeneity may provide a challenge for the data analysis. Results We propose using an efficient hybrid deep learning architecture convolutional neural network-long short-term memory, which combines with self-knowledge distillation to create highly accurate models to analyze the longitudinal microbiome profiles to predict disease outcomes. Using our proposed models, we analyzed the datasets from Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) study and DIABIMMUNE study. We showed the significant improvement in the area under the receiver operating characteristic curve scores, achieving 0.889 and 0.798 on PROTECT study and DIABIMMUNE study, respectively, compared with state-of-the-art temporal deep learning models. Our findings provide an effective artificial intelligence-based tool to predict disease outcomes using longitudinal microbiome profiles from collected patients. Availability and implementation The data and source code can be accessed at https://github.com/darylfung96/UC-disease-TL.
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Affiliation(s)
- Daryl L X Fung
- Department of Computer Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xu Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Carson K Leung
- Department of Computer Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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32
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Goswami K, Clarkson S, Tipton C, Phillips CD, Dennis DA, Klatt BA, O'Malley M, Smith EL, Gililland J, Pelt CE, Peters CL, Malkani AL, Palumbo BT, Lyons ST, Bernasek TL, Minter J, Goyal N, Purtill W, McDonald JF, Cross MB, Prieto HA, Lee GC, Hansen EN, Bini SA, Ward DT, Zhao N, Shohat N, Higuera CA, Nam D, Della Valle CJ, Parvizi J. The Microbiome of Osteoarthritic Hip and Knee Joints: A Prospective Multicenter Investigation. J Bone Joint Surg Am 2023; Publish Ahead of Print:00004623-990000000-00799. [PMID: 37192280 DOI: 10.2106/jbjs.22.00594] [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] [Indexed: 05/18/2023]
Abstract
BACKGROUND Recent advances in high-throughput DNA sequencing technologies have made it possible to characterize the microbial profile in anatomical sites previously assumed to be sterile. We used this approach to explore the microbial composition within joints of osteoarthritic patients. METHODS This prospective multicenter study recruited 113 patients undergoing hip or knee arthroplasty between 2017 and 2019. Demographics and prior intra-articular injections were noted. Matched synovial fluid, tissue, and swab specimens were obtained and shipped to a centralized laboratory for testing. Following DNA extraction, microbial 16S-rRNA sequencing was performed. RESULTS Comparisons of paired specimens indicated that each was a comparable measure for microbiological sampling of the joint. Swab specimens were modestly different in bacterial composition from synovial fluid and tissue. The 5 most abundant genera were Escherichia, Cutibacterium, Staphylococcus, Acinetobacter, and Pseudomonas. Although sample size varied, the hospital of origin explained a significant portion (18.5%) of the variance in the microbial composition of the joint, and corticosteroid injection within 6 months before arthroplasty was associated with elevated abundance of several lineages. CONCLUSIONS The findings revealed that prior intra-articular injection and the operative hospital environment may influence the microbial composition of the joint. Furthermore, the most common species observed in this study were not among the most common in previous skin microbiome studies, suggesting that the microbial profiles detected are not likely explained solely by skin contamination. Further research is needed to determine the relationship between the hospital and a "closed" microbiome environment. These findings contribute to establishing the baseline microbial signal and identifying contributing variables in the osteoarthritic joint, which will be valuable as a comparator in the contexts of infection and long-term arthroplasty success. LEVEL OF EVIDENCE Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Karan Goswami
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Samuel Clarkson
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Craig Tipton
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | | | - Brian A Klatt
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael O'Malley
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Eric L Smith
- New England Baptist Hospital, Chestnut Hill, Massachusetts
| | - Jeremy Gililland
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah
| | | | | | - Arthur L Malkani
- University of Louisville Adult Reconstruction Program, Louisville, Kentucky
| | - Brian T Palumbo
- University of South Florida Department of Orthopaedic Surgery, Clearwater, Florida
| | - Steven T Lyons
- University of South Florida Department of Orthopaedic Surgery, Clearwater, Florida
| | - Thomas L Bernasek
- University of South Florida Department of Orthopaedic Surgery, Clearwater, Florida
| | | | - Nitin Goyal
- Anderson Orthopaedic Research Institute, Alexandria, Virginia
| | - William Purtill
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | | | | | - Hernan A Prieto
- Department of Orthopaedics and Rehabilitation, University of Florida, Gainesville, Florida
| | - Gwo-Chin Lee
- Penn Presbyterian Medical Center, Philadelphia, Pennsylvania
| | - Erik N Hansen
- University of California San Francisco, San Francisco, California
| | - Stefano A Bini
- University of California San Francisco, San Francisco, California
| | - Derek T Ward
- University of California San Francisco, San Francisco, California
| | - Neil Zhao
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Noam Shohat
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Carlos A Higuera
- Department of Orthopaedic Surgery, Cleveland Clinic, Cleveland, Ohio
| | - Dennis Nam
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - Craig J Della Valle
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - Javad Parvizi
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
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Schwartz DJ, Shalon N, Wardenburg K, DeVeaux A, Wallace MA, Hall-Moore C, Ndao IM, Sullivan JE, Radmacher P, Escobedo M, D. Burnham CA, Warner BB, Tarr PI, Dantas G. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Sci Transl Med 2023; 15:eadg5562. [PMID: 37134153 PMCID: PMC10259202 DOI: 10.1126/scitranslmed.adg5562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]
Abstract
Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.
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Affiliation(s)
- Drew J. Schwartz
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nitan Shalon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kate Wardenburg
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna DeVeaux
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I. Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janice E. Sullivan
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children’s Hospital, Louisville, KY 40202, USA
| | - Paula Radmacher
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children’s Hospital, Louisville, KY 40202, USA
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma, Oklahoma City, OK 73117, USA
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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Briscoe L, Halperin E, Garud NR. SNV-FEAST: microbial source tracking with single nucleotide variants. Genome Biol 2023; 24:101. [PMID: 37121994 PMCID: PMC10150486 DOI: 10.1186/s13059-023-02927-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.
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Affiliation(s)
- Leah Briscoe
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Nandita R Garud
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA.
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Neyton LPA, Langelier CR, Calfee CS. Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses. Crit Care 2023; 27:90. [PMID: 36941644 PMCID: PMC10027598 DOI: 10.1186/s13054-023-04365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .
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Affiliation(s)
- Lucile P A Neyton
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Charles R Langelier
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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Xiong G, Ji L, Cheng M, Ning K. Niche-Based Microbial Community Assemblage in Urban Transit Systems and the Influence of City Characteristics. Microbiol Spectr 2023; 11:e0016723. [PMID: 36916942 PMCID: PMC10101094 DOI: 10.1128/spectrum.00167-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 03/16/2023] Open
Abstract
Microbiota residing on the urban transit systems (UTSs) can be shared by travelers and have niche-specific assemblage. However, it remains unclear how the assemblages are influenced by city characteristics, rendering city-specific and microbial-aware urban planning challenging. Here, we analyzed 3,359 UTS microbial samples collected from 16 cities around the world. We found the stochastic process dominated in all UTS microbiota assemblages, with the explanation rate (R2) of the neutral community model (NCM) higher than 0.7. Moreover, city characteristics predominantly drove such assemblage, largely responsible for the variation in the stochasticity ratio (50.1%). Furthermore, by utilizing an artificial intelligence model, we quantified the ability of UTS microbes in discriminating between cities and found that the ability was also strongly affected by city characteristics, especially climate and continent. From these, we found that although the NCM R2 of the New York City UTS microbiota was 0.831, the accuracy of the microbial-based city characteristic classifier was higher than 0.9. This is the first study to demonstrate the effects of city characteristics on the UTS microbiota assemblage, paving the way for city-specific and microbial-aware applications. IMPORTANCE We analyzed the urban transit system microbiota assemblage across 16 cities. The stochastic process was dominant in the urban transit system microbiota assemblage. The urban transit system microbe's ability in discriminating between cities was quantified using transfer learning based on random forest (RF) methods. Certain urban transit system microbes were strongly affected by city characteristics.
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Affiliation(s)
- Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Sah GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT. Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic. Microbiol Spectr 2023; 11:e0450922. [PMID: 36916973 PMCID: PMC10100919 DOI: 10.1128/spectrum.04509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/11/2023] [Indexed: 03/15/2023] Open
Abstract
The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.
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Affiliation(s)
- Govind Prasad Sah
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Lina Huang
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
| | - Susan Realegeno
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Scripps Institution of Oceanography and Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, San Diego, California, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
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França A. The Role of Coagulase-Negative Staphylococci Biofilms on Late-Onset Sepsis: Current Challenges and Emerging Diagnostics and Therapies. Antibiotics (Basel) 2023; 12:antibiotics12030554. [PMID: 36978421 PMCID: PMC10044083 DOI: 10.3390/antibiotics12030554] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Infections are one of the most significant complications of neonates, especially those born preterm, with sepsis as one of the principal causes of mortality. Coagulase-negative staphylococci (CoNS), a group of staphylococcal species that naturally inhabit healthy human skin and mucosa, are the most common cause of late-onset sepsis, especially in preterms. One of the risk factors for the development of CoNS infections is the presence of implanted biomedical devices, which are frequently used for medications and/or nutrient delivery, as they serve as a scaffold for biofilm formation. The major concerns related to CoNS infections have to do with the increasing resistance to multiple antibiotics observed among this bacterial group and biofilm cells’ increased tolerance to antibiotics. As such, the treatment of CoNS biofilm-associated infections with antibiotics is increasingly challenging and considering that antibiotics remain the primary form of treatment, this issue will likely persist in upcoming years. For that reason, the development of innovative and efficient therapeutic measures is of utmost importance. This narrative review assesses the current challenges and emerging diagnostic tools and therapies for the treatment of CoNS biofilm-associated infections, with a special focus on late-onset sepsis.
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Affiliation(s)
- Angela França
- Centre of Biological Engineering, LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, Braga and Guimarães, Portugal
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Lou YC, Hoff J, Olm MR, West-Roberts J, Diamond S, Firek BA, Morowitz MJ, Banfield JF. Using strain-resolved analysis to identify contamination in metagenomics data. MICROBIOME 2023; 11:36. [PMID: 36864482 PMCID: PMC9979413 DOI: 10.1186/s40168-023-01477-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/28/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported. RESULTS Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass. CONCLUSION Our work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jordan Hoff
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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Effects of Perinatal Antibiotic Exposure and Neonatal Gut Microbiota. Antibiotics (Basel) 2023; 12:antibiotics12020258. [PMID: 36830169 PMCID: PMC9951864 DOI: 10.3390/antibiotics12020258] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Antibiotic therapy is one of the most important strategies to treat bacterial infections. The overuse of antibiotics, especially in the perinatal period, is associated with long-lasting negative consequences such as the spread of antibiotic resistance and alterations in the composition and function of the gut microbiota, both of which negatively affect human health. In this review, we summarize recent evidence about the influence of antibiotic treatment on the neonatal gut microbiota and the subsequent negative effects on the health of the infant. We also analyze the possible microbiome-based approaches for the re-establishment of healthy microbiota in neonates.
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Mercer EM, Arrieta MC. Probiotics to improve the gut microbiome in premature infants: are we there yet? Gut Microbes 2023; 15:2201160. [PMID: 37122152 PMCID: PMC10153018 DOI: 10.1080/19490976.2023.2201160] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Gut microbiome maturation in infants born prematurely is uniquely influenced by the physiological, clinical, and environmental factors surrounding preterm birth and early life, leading to altered patterns of microbial succession relative to term infants during the first months of life. These differences in microbiome composition are implicated in acute clinical conditions that disproportionately affect preterm infants, including necrotizing enterocolitis (NEC) and late-onset sepsis (LOS). Probiotic supplementation initiated early in life is an effective prophylactic measure for preventing NEC, LOS, and other clinical concerns relevant to preterm infants. In parallel, reported benefits of probiotics on the preterm gut microbiome, metabolome, and immune function are beginning to emerge. This review summarizes the current literature on the influence of probiotics on the gut microbiome of preterm infants, outlines potential mechanisms by which these effects are exerted, and highlights important clinical considerations for determining the best practices for probiotic use in premature infants.
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Affiliation(s)
- Emily M. Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
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42
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Sex differences in the oral microbiome, host traits, and their causal relationships. iScience 2022; 26:105839. [PMID: 36660475 PMCID: PMC9843272 DOI: 10.1016/j.isci.2022.105839] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/09/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The oral microbiome has been implicated in a growing number of diseases; however, determinants of the oral microbiome and their roles remain elusive. Here, we investigated the oral (saliva and tongue dorsum) metagenome, the whole genome, and other omics data in a total of 4,478 individuals and demonstrated that the oral microbiome composition and its major contributing host factors significantly differed between sexes. We thus conducted a sex-stratified metagenome-genome-wide-association study (M-GWAS) and identified 11 differential genetic associations with the oral microbiome (p sex-difference < 5 × 10-8). Furthermore, we performed sex-stratified Mendelian randomization (MR) analyses and identified abundant causalities between the oral microbiome and serum metabolites. Notably, sex-specific microbes-hormonal interactions explained the mostly observed sex hormones differences such as the significant causalities enrichments for aldosterone in females and androstenedione in males. These findings illustrate the necessity of sex stratification and deepen our understanding of the interplay between the oral microbiome and serum metabolites.
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Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. MICROBIOME 2022; 10:206. [PMID: 36457108 PMCID: PMC9716758 DOI: 10.1186/s40168-022-01412-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA.
| | - Alexander G McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Ryan A Blaustein
- Department of Nutrition and Food Science, University of Maryland, College Park, USA
| | - Laura J Rose
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
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Ding J, Ouyang R, Zheng S, Wang Y, Huang Y, Ma X, Zou Y, Chen R, Zhuo Z, Li Z, Xin Q, Zhou L, Mei S, Yan J, Lu X, Ren Z, Liu X, Xu G. Effect of Breastmilk Microbiota and Sialylated Oligosaccharides on the Colonization of Infant Gut Microbial Community and Fecal Metabolome. Metabolites 2022; 12:1136. [PMID: 36422276 PMCID: PMC9698434 DOI: 10.3390/metabo12111136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 07/30/2023] Open
Abstract
The complex microbiota and sialylated oligosaccharides in breastmilk are important bioactive components that affect the gut microbiota. However, the effect of breastmilk microbiota and sialylated oligosaccharides on the gut microbiota during the neonatal period has been largely overlooked. Here, 16S rRNA gene sequencing and metabolomics analysis were applied to the breastmilk and feces of 69 newborns to clarify the link between breastmilk components and the newborn gut. Results showed that Staphylococcus, Enterococcus, and Bacteroides were commonly shared and positively correlated between breastmilk and the neonatal intestine and they were the main bacteria of breastmilk that interacted with the newborn fecal metabolome. Breastmilk Staphylococcus mainly interacted with amino acids, whereas Bacteroides was involved in the tryptophan, nucleotide, and vitamin metabolism. Breastmilk sialylated oligosaccharides were related to Bacteroides and amino acids of the newborn fecal metabolites. Moreover, Bacteroides was related to the interaction between breastmilk 3'-sialyllactose and newborn fecal metabolites in the mediation effect models. Finally, we pointed out that breastmilk Bacteroides was important in the milk-gut interaction, and it was negatively associated with waist circumference in infants aged 1 year. Our study provides a scientific basis for understanding the role of breastmilk in the development of newborn gut microbiota and metabolome.
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Affiliation(s)
- Juan Ding
- Department of Quality Control, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Runze Ouyang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Yanfeng Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Yan Huang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Ma
- Department of Nursing, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yuxin Zou
- Liaocheng People’s Hospital, Liaocheng 252000, China
| | - Rong Chen
- Dalian Municipal Women and Children’s Medical Center (Group), Dalian 116011, China
| | - Zhihong Zhuo
- Department of Pediatric, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhen Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Qi Xin
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Surong Mei
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingyu Yan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
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Vongbhavit K, Salinero LK, Kalanetra KM, Masarweh C, Yu A, Taft DH, Mills DA, Underwood MA. A comparison of bacterial colonization between nasogastric and orogastric enteral feeding tubes in infants in the neonatal intensive care unit. J Perinatol 2022; 42:1446-1452. [PMID: 35840710 PMCID: PMC9616717 DOI: 10.1038/s41372-022-01452-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Feeding tubes harbor microbial contaminants; studies to date have not explored differences between orogastric (OG) and nasogastric (NG) tube biofilms. We sought to extend a previous analysis by comparing bacterial colonization by location (OG v NG) and by evaluating clinical factors that may affect tube bacterial populations. STUDY DESIGN The pharyngeal segments of 41 infant feeding tubes (14 OG and 27 NG) from 41 infants were analyzed by next generation 16 S rRNA sequencing on the MiSeq platform. RESULTS At the phylum level, Proteobacteria had the highest relative abundance of both OG and NG tubes. At the genus/species level, nine taxa differed significantly between OG and NG tubes. Alpha and beta diversity analyses showed significant differences between OG and NG tubes with relatively little contribution from clinical factors. CONCLUSION The route of feeding tube insertion (oral vs nasal) had a greater impact on bacterial colonization than the assessed clinical factors.
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Affiliation(s)
- Kannikar Vongbhavit
- Department of Pediatrics, HRH Princess Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Nakornayok, Thailand
- Division of Neonatology, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Lauren K Salinero
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Karen M Kalanetra
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Chad Masarweh
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Alice Yu
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Diana H Taft
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - David A Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Mark A Underwood
- Division of Neonatology, Department of Pediatrics, University of California Davis, Sacramento, CA, USA.
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MDITRE: Scalable and Interpretable Machine Learning for Predicting Host Status from Temporal Microbiome Dynamics. mSystems 2022; 7:e0013222. [PMID: 36069455 PMCID: PMC9600536 DOI: 10.1128/msystems.00132-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Longitudinal microbiome data sets are being generated with increasing regularity, and there is broad recognition that these studies are critical for unlocking the mechanisms through which the microbiome impacts human health and disease. However, there is a dearth of computational tools for analyzing microbiome time-series data. To address this gap, we developed an open-source software package, Microbiome Differentiable Interpretable Temporal Rule Engine (MDITRE), which implements a new highly efficient method leveraging deep-learning technologies to derive human-interpretable rules that predict host status from longitudinal microbiome data. Using semi-synthetic and a large compendium of publicly available 16S rRNA amplicon and metagenomics sequencing data sets, we demonstrate that in almost all cases, MDITRE performs on par with or better than popular uninterpretable machine learning methods, and orders-of-magnitude faster than the prior interpretable technique. MDITRE also provides a graphical user interface, which we show through case studies can be used to derive biologically meaningful interpretations linking patterns of microbiome changes over time with host phenotypes. IMPORTANCE The human microbiome, or collection of microbes living on and within us, changes over time. Linking these changes to the status of the human host is crucial to understanding how the microbiome influences a variety of human diseases. Due to the large scale and complexity of microbiome data, computational methods are essential. Existing computational methods for linking changes in the microbiome to the status of the human host are either unable to scale to large and complex microbiome data sets or cannot produce human-interpretable outputs. We present a new computational method and software package that overcomes the limitations of previous methods, allowing researchers to analyze larger and more complex data sets while producing easily interpretable outputs. Our method has the potential to enable new insights into how changes in the microbiome over time maintain health or lead to disease in humans and facilitate the development of diagnostic tests based on the microbiome.
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Zeng S, Patangia D, Almeida A, Zhou Z, Mu D, Paul Ross R, Stanton C, Wang S. A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. Nat Commun 2022; 13:5139. [PMID: 36050292 PMCID: PMC9437082 DOI: 10.1038/s41467-022-32805-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life. Here the authors present a large-scale resource of the early-life human gut microbiome from children under three years old, which comprises 32,277 metagenome-assembled gut genomes, representing 2172 species, and more than 80 million gut proteins representing >4 million protein clusters, spanning multiple clinical factors including age, delivery mode, gestational age, and feeding patterns.
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Affiliation(s)
- Shuqin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Dhrati Patangia
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Zhemin Zhou
- Pasteurien College, Medical College of Soochow University, Soochow University, Suzhou, China
| | - Dezhi Mu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
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Guitor AK, Yousuf EI, Raphenya AR, Hutton EK, Morrison KM, McArthur AG, Wright GD, Stearns JC. Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. MICROBIOME 2022; 10:136. [PMID: 36008821 PMCID: PMC9414150 DOI: 10.1186/s40168-022-01327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. RESULTS At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. CONCLUSIONS This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.
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Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Jennifer C Stearns
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada.
- Department of Medicine, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
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Zhang L, Jonscher KR, Zhang Z, Xiong Y, Mueller RS, Friedman JE, Pan C. Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes. Nat Commun 2022; 13:3551. [PMID: 35729161 PMCID: PMC9213500 DOI: 10.1038/s41467-022-31227-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/09/2022] [Indexed: 12/13/2022] Open
Abstract
The immune system of some genetically susceptible children can be triggered by certain environmental factors to produce islet autoantibodies (IA) against pancreatic β cells, which greatly increases their risk for Type-1 diabetes. An environmental factor under active investigation is the gut microbiome due to its important role in immune system education. Here, we study gut metagenomes that are de-novo-assembled in 887 at-risk children in the Environmental Determinants of Diabetes in the Young (TEDDY) project. Our results reveal a small set of core protein families, present in >50% of the subjects, which account for 64% of the sequencing reads. Time-series binning generates 21,536 high-quality metagenome-assembled genomes (MAGs) from 883 species, including 176 species that hitherto have no MAG representation in previous comprehensive human microbiome surveys. IA seroconversion is positively associated with 2373 MAGs and negatively with 1549 MAGs. Comparative genomics analysis identifies lipopolysaccharides biosynthesis in Bacteroides MAGs and sulfate reduction in Anaerostipes MAGs as functional signatures of MAGs with positive IA-association. The functional signatures in the MAGs with negative IA-association include carbohydrate degradation in lactic acid bacteria MAGs and nitrate reduction in Escherichia MAGs. Overall, our results show a distinct set of gut microorganisms associated with IA seroconversion and uncovered the functional genomics signatures of these IA-associated microorganisms.
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Affiliation(s)
- Li Zhang
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Karen R Jonscher
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zuyuan Zhang
- School of Computer Science, University of Oklahoma, Norman, OK, USA
| | - Yi Xiong
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Jacob E Friedman
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Chongle Pan
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA. .,School of Computer Science, University of Oklahoma, Norman, OK, USA.
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50
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Sukhum KV, Newcomer EP, Cass C, Wallace MA, Johnson C, Fine J, Sax S, Barlet MH, Burnham CAD, Dantas G, Kwon JH. Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates. COMMUNICATIONS MEDICINE 2022; 2:62. [PMID: 35664456 PMCID: PMC9160058 DOI: 10.1038/s43856-022-00124-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/06/2022] [Indexed: 02/03/2023] Open
Abstract
Background Healthcare-associated infections due to antibiotic-resistant organisms pose an acute and rising threat to critically ill and immunocompromised patients. To evaluate reservoirs of antibiotic-resistant organisms as a source of transmission to patients, we interrogated isolates from environmental surfaces, patient feces, and patient blood infections from an established and a newly built intensive care unit. Methods We used selective culture to recover 829 antibiotic-resistant organisms from 1594 environmental and 72 patient fecal samples, in addition to 81 isolates from blood cultures. We conducted antibiotic susceptibility testing and short- and long-read whole genome sequencing on recovered isolates. Results Antibiotic-resistant organism burden is highest in sink drains compared to other surfaces. Pseudomonas aeruginosa is the most frequently cultured organism from surfaces in both intensive care units. From whole genome sequencing, different lineages of P. aeruginosa dominate in each unit; one P. aeruginosa lineage of ST1894 is found in multiple sink drains in the new intensive care unit and 3.7% of blood isolates analyzed, suggesting movement of this clone between the environment and patients. Conclusions These results highlight antibiotic-resistant organism reservoirs in hospital built environments as an important target for infection prevention in hospitalized patients.
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Affiliation(s)
- Kimberley V. Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Erin P. Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO USA
| | - Candice Cass
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Caitlin Johnson
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Jeremy Fine
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Steven Sax
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Margaret H. Barlet
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO USA
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, MO USA
| | - Jennie H. Kwon
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO USA
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