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Cui M, Guo Q, Zhao S, Liu X, Yang C, Liu P, Wang L. An untargeted comparative metabolomics analysis of infants with and without late-onset breast milk jaundice. PLoS One 2024; 19:e0308710. [PMID: 39133689 PMCID: PMC11318923 DOI: 10.1371/journal.pone.0308710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Late-onset breast milk jaundice (LBMJ) is a common form of hyperbilirubinemia, which can result in serious complications for newborns with persistently high bilirubin levels. The aim of this study was to investigate the differences in fecal metabolites between breastfed infants with and without LBMJ in order to elucidate potential biological mechanisms. METHODS Biological samples were collected from 12 infants with LBMJ and 12 healthy individuals. Ultra-high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF/MS) was utilized for non-targeted determination of fecal metabolites. Principal components analysis (PCA), cluster analysis, and differential metabolite analysis were performed in both positive ion mode and negative ion mode for the two groups. Additionally, the KEGG database was employed to comprehensively analyze the pathways of differential metabolites. RESULTS There were no significant differences in maternal and neonatal demographic characteristics between the two groups (p > 0.05). The results of PCA and cluster heat map analysis in both modes showed that there were significant differences in metabolites between the two groups. Among 751 differential metabolites (DMs) detected in positive ion mode, 720 were up-regulated in the case group while 31 were down-regulated. In negative ion mode, 1891 DMs were detected, including 817 up-regulated metabolites and 1074 down-regulated metabolites in the case group. Analysis of differential metabolic pathways showed that the DMs of the two groups were mainly annotated and enriched in Biotin metabolism, N-Glycan biosynthesis, Taurine and hypotaurine metabolism, Pyrimidine metabolism, and Pentose and glucuronate interconversions. CONCLUSION Significant differences exist in fecal metabolites between LBMJ infants and healthy controls. The study of differential metabolic pathways provides insights into the mechanism of LBMJ.
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Affiliation(s)
- Mingxuan Cui
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Qianying Guo
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Shilong Zhao
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Xinran Liu
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Chen Yang
- Institute of Reproductive and Child Health/National Health Commission Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing, China
| | - Peng Liu
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Linlin Wang
- Institute of Reproductive and Child Health/National Health Commission Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing, China
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D’Amico F, Rinaldi M, Pascale R, Fabbrini M, Morelli MC, Siniscalchi A, Laici C, Coladonato S, Ravaioli M, Cescon M, Ambretti S, Viale P, Brigidi P, Turroni S, Giannella M. Gut microbiome dynamics and Enterobacterales infection in liver transplant recipients: A prospective observational study. JHEP Rep 2024; 6:101039. [PMID: 38524669 PMCID: PMC10960129 DOI: 10.1016/j.jhepr.2024.101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 03/26/2024] Open
Abstract
Background & Aims The aim of this study was to investigate gut microbiome (GM) dynamics in relation to carbapenem-resistant Enterobacterales (CRE) colonization, CRE infection, and non-CRE infection development within 2 months after liver transplant (LT). Methods A single-center, prospective study was performed in patients undergoing LT from November 2018 to January 2020. The GM was profiled through 16S rRNA amplicon sequencing of a rectal swab taken on the day of transplantation, and fecal samples were collected weekly until 1 month after LT. A subset of samples was subjected to shotgun metagenomics, including resistome dynamics. The primary endpoint was to explore changes in the GM in the following groups: (1) CRE carriers developing CRE infection (CRE_I); (2) CRE carriers not developing infection (CRE_UI); (3) non-CRE carriers developing microbial infection (INF); and (4) non-CRE carriers not developing infection (NEG). Results Overall, 97 patients were enrolled, and 91 provided fecal samples. Of these, five, nine, 22, and 55 patients were classified as CRE_I, CRE_UI, INF, and NEG, respectively. CRE_I patients showed an immediate and sustained post-LT decrease in alpha diversity, with depletion of the GM structure and gradual over-representation of Klebsiella and Enterococcus. The proportions of Klebsiella were significantly higher in CRE_I patients than in NEG patients even before LT, serving as an early marker of subsequent CRE infection. CRE_UI patients had a more stable and diverse GM, whose compositional dynamics tended to overlap with those of NEG patients. Conclusions GM profiling before LT could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis. Impact and implications Little is known about the temporal dynamics of gut microbiome (GM) in liver transplant recipients associated with carbapenem-resistant Enterobacterales (CRE) colonization and infection. The GM structure and functionality of patients colonized with CRE and developing infection appeared to be distinct compared with CRE carriers without infection or patients with other microbial infection or no infection and CRE colonization. Higher proportions of antimicrobial-resistant pathogens and poor representation of bacteria and metabolic pathways capable of promoting overall host health were observed in CRE carriers who developed infection, even before liver transplant. Therefore, pretransplant GM profiling could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis.
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Affiliation(s)
- Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Matteo Rinaldi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Renato Pascale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maria Cristina Morelli
- Internal Medicine Unit for the Treatment of Severe Organ Failure, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Antonio Siniscalchi
- Division of Anesthesiology, Department of Anesthesia and Intensive Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Cristiana Laici
- Division of Anesthesiology, Department of Anesthesia and Intensive Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simona Coladonato
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Matteo Ravaioli
- General Surgery and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Matteo Cescon
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- General Surgery and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Simone Ambretti
- Microbiology Operative Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Pierluigi Viale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maddalena Giannella
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Integrated Management of Infectious Risk, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico Sant'Orsola, Bologna, Italy
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Liu Q, Chen Y, Xu XW. Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches. Front Microbiol 2023; 14:1273211. [PMID: 38156017 PMCID: PMC10753782 DOI: 10.3389/fmicb.2023.1273211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.
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Affiliation(s)
- Qian Liu
- Donghai Laboratory, Zhoushan, Zhejiang, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuhao Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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Nagar S, Bharti M, Negi RK. Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring. Appl Microbiol Biotechnol 2023; 107:3273-3289. [PMID: 37052633 DOI: 10.1007/s00253-023-12503-6] [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: 10/28/2022] [Revised: 03/18/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023]
Abstract
The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, India
| | - Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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Walker A, Schmitt-Kopplin P. The role of fecal sulfur metabolome in inflammatory bowel diseases. Int J Med Microbiol 2021; 311:151513. [PMID: 34147944 DOI: 10.1016/j.ijmm.2021.151513] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/22/2021] [Accepted: 05/17/2021] [Indexed: 12/17/2022] Open
Abstract
Sulfur metabolism and sulfur-containing metabolites play an important role in the human digestive system, and sulfur compounds and pathways are associated with inflammatory bowel diseases (IBD). In fact, cysteine metabolism results in the production of taurine and sulfate, and gut microbes catabolize them into hydrogen sulfide, a signaling molecule with various biological functions. Besides metabolites originating from sulfur metabolism, several other sulfur-containing metabolites of different classes were detected in human feces, consisting of non-volatile and volatile compounds. Sulfated steroids and bile acids such as taurine-conjugated bile acids are the major classes along with sulfur amino acids and sulfur-containing peptides. Indeed, sulfur-containing metabolites were described in stool samples from healthy subjects, patients suffering from colorectal cancer or IBD. In metabolomics-driven studies, around 50 known sulfur-containing metabolites were linked to IBD. Taurine, taurocholic acid, taurochenodeoxycholic acid, methionine, methanethiol and hydrogen sulfide were regularly reported in IBD studies, and most of them were elevated in stool samples from IBD patients. We summarized from this review that there is strong interplay between perturbed gut microbiota in IBD, and the consistently higher abundance of sulfur-containing metabolites, which potentially represent substrates for sulfidogenic bacteria such as Bilophila or Escherichia and promote their growth. These bacteria might shift their metabolism towards the degradation of taurine and cysteine and therefore to a higher hydrogen sulfide production.
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Affiliation(s)
- Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany; ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany; Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany
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