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Horváthová T, Lafuente E, Bartels JA, Wallisch J, Vorburger C. Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome. Environ Microbiol Rep 2024; 16:e13252. [PMID: 38783543 DOI: 10.1111/1758-2229.13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.
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Affiliation(s)
- Terézia Horváthová
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
- Institute of Soil Biology and Biochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Elvira Lafuente
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jo-Anne Bartels
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Jesper Wallisch
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
- D-USYS, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Pastar I, Jimenez F, Erdmann H, Bosch TCG, Paus R. Spatial Distribution and Functional Impact of Human Scalp Hair Follicle Microbiota. J Invest Dermatol 2024; 144:1353-1367.e15. [PMID: 38070726 DOI: 10.1016/j.jid.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 02/26/2024]
Abstract
Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbiota contaminants or assess the HF microbiota incompletely, and microbiota functions in human HF physiology remain ill explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage-, and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes, and Malassezia restricta, with the latter 2 being the most abundant viable HF colonizers (as tested by propidium monoazide assay) and, surprisingly, most abundant in the HF mesenchyme. Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism, and melanogenesis, suggesting that selected microbial products may modulate HF functions. Indeed, HF treatment with butyrate, a metabolite of S. epidermidis and other HF microbiota, delayed catagen and promoted autophagy, mitochondrial activity, and gp100 and dermcidin expression ex vivo. Thus, human HF microbiota show spatial variations in abundance and modulate the physiology of their host, which invites therapeutic targeting.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Münster, Germany; Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Tim Lachnit
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Irena Pastar
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Francisco Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain; Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | - Ralf Paus
- Monasterium Laboratory, Münster, Germany; Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA; CUTANEON, Hamburg, Germany.
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Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR. The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk. mSystems 2024:e0115823. [PMID: 38785438 DOI: 10.1128/msystems.01158-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
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Affiliation(s)
- C J Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Y Deng
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T C Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - F Pena-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B A Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - S M Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L S Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N R Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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Beneke V, Grieger KM, Hartwig C, Müller J, Sohn K, Blaudszun AR, Hilger N, Schaudien D, Fricke S, Braun A, Sewald K, Hesse C. Homeostatic T helper 17 cell responses triggered by complex microbiota are maintained in ex vivo intestinal tissue slices. Eur J Immunol 2024:e2350946. [PMID: 38763899 DOI: 10.1002/eji.202350946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
Segmented filamentous bacteria (SFB) are members of the commensal intestinal microbiome. They are known to contribute to the postnatal maturation of the gut immune system, but also to augment inflammatory conditions in chronic diseases such as Crohn's disease. Living primary tissue slices are ultrathin multicellular sections of the intestine and provide a unique opportunity to analyze tissue-specific immune responses ex vivo. This study aimed to investigate whether supplementation of the gut flora with SFB promotes T helper 17 (Th17) cell responses in primary intestinal tissue slices ex vivo. Primary tissue slices were prepared from the small intestine of healthy Taconic mice with SFB-positive and SFB-negative microbiomes and stimulated with anti-CD3/CD28 or Concanavalin A. SFB-positive and -negative mice exhibited distinct microbiome compositions and Th17 cell frequencies in the intestine and complex microbiota including SFB induced up to 15-fold increase in Th17 cell-associated mediators, serum amyloid A (SAA), and immunoglobulin A (IgA) responses ex vivo. This phenotype could be transmitted by co-housing of mice. Our findings highlight that changes in the gut microbiome can be observed in primary intestinal tissue slices ex vivo. This makes the system very attractive for disease modeling and assessment of new therapies.
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Affiliation(s)
- Valerie Beneke
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
| | - Klaudia M Grieger
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
| | - Christina Hartwig
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Jan Müller
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
- Center of Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Member of the Vienna Biocenter PhD Program, University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Kai Sohn
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - André-René Blaudszun
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Nadja Hilger
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dirk Schaudien
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Stephan Fricke
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Armin Braun
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Institute for Immunology, Hannover Medical School, Hannover, Germany
| | - Katherina Sewald
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
| | - Christina Hesse
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
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Min K, Glowacki AJ, Bosma ML, McGuire JA, Tian S, McAdoo K, DelSasso A, Fourre T, Gambogi RJ, Milleman J, Milleman KR. Quantitative analysis of the effects of essential oil mouthrinses on clinical plaque microbiome: a parallel-group, randomized trial. BMC Oral Health 2024; 24:578. [PMID: 38762482 PMCID: PMC11102605 DOI: 10.1186/s12903-024-04365-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND The rich diversity of microorganisms in the oral cavity plays an important role in the maintenance of oral health and development of detrimental oral health conditions. Beyond commonly used qualitative microbiome metrics, such as relative proportions or diversity, both the species-level identification and quantification of bacteria are key to understanding clinical disease associations. This study reports the first-time application of an absolute quantitative microbiome analysis using spiked DNA standards and shotgun metagenome sequencing to assess the efficacy and safety of product intervention on dental plaque microbiome. METHODS In this parallel-group, randomized clinical trial, essential oil mouthrinses, including LISTERINE® Cool Mint Antiseptic (LCM), an alcohol-containing prototype mouthrinse (ACPM), and an alcohol-free prototype mouthrinse (AFPM), were compared against a hydroalcohol control rinse on clinical parameters and the oral microbiome of subjects with moderate gingivitis. To enable a sensitive and clinically meaningful measure of bacterial abundances, species were categorized according to their associations with oral conditions based on published literature and quantified using known amounts of spiked DNA standards. RESULTS Multivariate analysis showed that both LCM and ACPM shifted the dysbiotic microbiome composition of subjects with gingivitis to a healthier state after 4 weeks of twice-daily use, resembling the composition of subjects with clinically healthy oral conditions recruited for observational reference comparison at baseline. The essential oil-containing mouthrinses evaluated in this study showed statistically significant reductions in clinical gingivitis and plaque measurements when compared to the hydroalcohol control rinse after 6 weeks of use. CONCLUSIONS By establishing a novel quantitative method for microbiome analysis, this study sheds light on the mechanisms of LCM mouthrinse efficacy on oral microbial ecology, demonstrating that repeated usage non-selectively resets a gingivitis-like oral microbiome toward that of a healthy oral cavity. TRIAL REGISTRATION The trial was registered on ClinicalTrials.gov on 10/06/2021. The registration number is NCT04921371.
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Affiliation(s)
- Kyungrok Min
- Johnson & Johnson Consumer Inc, Skillman, NJ, USA.
| | | | | | | | - Sandy Tian
- Johnson & Johnson Consumer Inc, Skillman, NJ, USA
| | | | | | - Tara Fourre
- Johnson & Johnson Consumer Inc, Skillman, NJ, USA
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024:1-14. [PMID: 38772736 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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Li X, Liu C, Wang D, Deng J, Guo Y, Shen Y, Yang S, Ji JS, Luo H, Bai J, Jiang J. Persistent pollution of genetic materials in a typical laboratory environment. J Hazard Mater 2024; 470:134201. [PMID: 38579585 DOI: 10.1016/j.jhazmat.2024.134201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/20/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
From the onset of coronavirus disease (COVID-19) pandemic, there are concerns regarding the disease spread and environmental pollution of biohazard since studies on genetic engineering flourish and numerous genetic materials were used such as the nucleic acid test of the severe acute respiratory syndrome coronavirus (SARS-CoV-2). In this work, we studied genetic material pollution in an institute during a development cycle of plasmid, one of typical genetic materials, with typical laboratory settings. The pollution source, transmission routes, and pollution levels in laboratory environment were examined. The Real-Time quantitative- Polymerase Chain Reaction results of all environmental mediums (surface, aerosol, and liquid) showed that a targeted DNA segment occurred along with routine experimental operations. Among the 79 surface and air samples collected in the genetic material operation, half of the environment samples (38 of 79) are positive for nucleic acid pollution. Persistent nucleic acid contaminations were observed in all tested laboratories and spread in the public area (hallway). The highest concentration for liquid and surface samples were 1.92 × 108 copies/uL and 5.22 × 107 copies/cm2, respectively. Significant amounts of the targeted gene (with a mean value of 74 copies/L) were detected in the indoor air of laboratories utilizing centrifuge devices, shaking tables, and cell homogenizers. Spills and improper disposal of plasmid products were primary sources of pollution. The importance of establishing designated experimental zones, employing advanced biosafety cabinets, and implementing highly efficient cleaning systems in laboratories with lower biosafety levels is underscored. SYNOPSIS: STATEMENT. Persistent environmental pollutions of genetic materials are introduced by typical experiments in laboratories with low biosafety level.
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Affiliation(s)
- Xue Li
- School of Environment, Tsinghua University, Beijing, China
| | - Ce Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Dongbin Wang
- School of Environment, Tsinghua University, Beijing, China
| | - Jianguo Deng
- School of Environment, Tsinghua University, Beijing, China
| | - Yuntao Guo
- Department of Electrical Engineering, Tsinghua University, Beijing, China
| | - Yicheng Shen
- School of Environment, Tsinghua University, Beijing, China
| | - Shuwen Yang
- School of Environment, Tsinghua University, Beijing, China
| | - John S Ji
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Haiyun Luo
- Department of Electrical Engineering, Tsinghua University, Beijing, China
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jingkun Jiang
- School of Environment, Tsinghua University, Beijing, China.
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Varela JL, Nikouli E, Medina A, Papaspyrou S, Kormas K. The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean. Int Microbiol 2024:10.1007/s10123-024-00524-8. [PMID: 38740652 DOI: 10.1007/s10123-024-00524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.
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Affiliation(s)
- José Luis Varela
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Antonio Medina
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Sokratis Papaspyrou
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 382 21, Volos, Greece.
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Launes C, Camacho J, Pons-Espinal M, López-Labrador FX, Esteva C, Cabrerizo M, Fernández-García MD, Fogeda M, Masa-Calles J, López-Perea N, Echevarría JE, Muñoz-Almagro C, Tarragó D. Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis. Eur J Clin Microbiol Infect Dis 2024; 43:863-873. [PMID: 38438704 PMCID: PMC11108891 DOI: 10.1007/s10096-024-04795-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE Investigation of undiagnosed cases of infectious neurological diseases, especially in the paediatric population, remains a challenge. This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and/or encephalitis (M/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture (HCSS). METHODS A single-centre prospective study was conducted at Sant Joan de Déu University Hospital, Barcelona, involving 40 M/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis/Encephalitis Panel. HCSS was used to detect viral nucleic acid in the patients' CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines. RESULTS Forty episodes of M/ME of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113 detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections. CONCLUSION This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.
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Affiliation(s)
- Cristian Launes
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Departament de Medicina i Especialitats Medicoquirúrgiques, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | - Marina Pons-Espinal
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - F Xavier López-Labrador
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Genomics & Health Department, FISABIO-Public Health Foundation, Valencia, Spain
- Department of Microbiology and Ecology, Medical School, University of Valencia, Valencia, Spain
| | - Cristina Esteva
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - María Cabrerizo
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | - María Dolores Fernández-García
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | | | - Josefa Masa-Calles
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Avda Monforte de Lemos 5, Madrid, Spain
| | - Noemí López-Perea
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Avda Monforte de Lemos 5, Madrid, Spain
| | - Juan Emilio Echevarría
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - David Tarragó
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain.
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10
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Foessleitner P, Pjevac P, Granser S, Wisgrill L, Pummer L, Eckel F, Seki D, Berry D, Hausmann B, Farr A. The maternal microbiome in pregnancy, delivery, and early-stage development of neonatal microbiome after cesarean section: A prospective longitudinal study. Acta Obstet Gynecol Scand 2024; 103:832-841. [PMID: 38268221 PMCID: PMC11019516 DOI: 10.1111/aogs.14773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Changes within the maternal microbiome during the last trimester of pregnancy and the determinants of the subsequent neonatal microbiome establishment after delivery by elective cesarean section are described. MATERIAL AND METHODS Maternal vaginal and rectal microbiome samples were collected in the last trimester and before cesarean section; intrauterine cavity, placenta, neonatal buccal mucosa, skin, and meconium samples were obtained at birth; neonatal sample collection was repeated 2-3 days postnatally. Microbial community composition was analyzed by 16S rRNA gene amplicon sequencing. Relative abundance measurements of amplicon sequencing variants and sum counts at higher taxonomic levels were compared to test for significant overlap or differences in microbial community compositions. CLINICALTRIALS gov ID: NCT04489056. RESULTS A total of 30 mothers and their neonates were included with available microbiome samples for all maternal, intrauterine cavity and placenta samples, as well as for 18 of 30 neonates. The composition of maternal vaginal and rectal microbiomes during the last trimester of healthy pregnancies did not significantly change (permutational multivariate analysis of variance [PERMANOVA], p > 0.05). No robust microbial signature was detected in the intrauterine cavity, placenta, neonatal buccal mucosa, skin swabs, or meconium samples collected at birth. After birth, the neonatal microbiome was rapidly established, and significantly different microbial communities were detectable 2-3 days postnatally in neonate buccal mucosa and stool samples (PERMANOVA, p < 0.01). CONCLUSIONS Maternal vaginal and rectal microbiomes in healthy pregnancies remain stable during the third trimester. No microbial colonization of the neonate was observed before birth in healthy pregnancies. Neonatal microbiomes in infants delivered by cesarean section displayed a taxonomic composition distinct from maternal vaginal and rectal microbiomes at birth, indicating that postnatal exposure to the extrauterine environment is the driving source of initial neonatal microbiome development in this cohort.
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Affiliation(s)
- Philipp Foessleitner
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
| | - Petra Pjevac
- Joint Microbiome FacilityMedical University of Vienna and University of ViennaViennaAustria
- University of ViennaCenter for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem ScienceViennaAustria
| | - Sonja Granser
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
| | - Lukas Wisgrill
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Intensive Care Medicine, and Neuropediatrics, and Comprehensive Center for Pediatrics (CCP)Medical University of ViennaViennaAustria
| | - Lisa Pummer
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Intensive Care Medicine, and Neuropediatrics, and Comprehensive Center for Pediatrics (CCP)Medical University of ViennaViennaAustria
| | - Fanny Eckel
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
| | - David Seki
- University of ViennaCenter for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem ScienceViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - David Berry
- Joint Microbiome FacilityMedical University of Vienna and University of ViennaViennaAustria
- University of ViennaCenter for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem ScienceViennaAustria
| | - Bela Hausmann
- Joint Microbiome FacilityMedical University of Vienna and University of ViennaViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Alex Farr
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
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11
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Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, Wokaty J, Gamboa-Tuz SD, Sengupta P, Hecht I, Ravikrishnan A, Gonçalves RS, Franzosa E, Raman K, Carey V, Dowd JB, Jones HE, Davis S, Segata N, Huttenhower C, Waldron L. BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nat Biotechnol 2024; 42:790-802. [PMID: 37697152 PMCID: PMC11098749 DOI: 10.1038/s41587-023-01872-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/20/2023] [Indexed: 09/13/2023]
Abstract
The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures. These data allow assessment of microbiome differential abundance within and across experimental conditions, environments or body sites. Database-wide analysis reveals experimental conditions with the highest level of consistency in signatures reported by independent studies and identifies commonalities among disease-associated signatures, including frequent introgression of oral pathobionts into the gut.
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Affiliation(s)
- Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Chloe Mirzayi
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Fatima Zohra
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Rimsha Azhar
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Shaimaa Elsafoury
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Clare Grieve
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Jennifer Wokaty
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Samuel David Gamboa-Tuz
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
| | | | - Aarthi Ravikrishnan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Rafael S Gonçalves
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Eric Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Vincent Carey
- Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston, MA, USA
| | - Jennifer B Dowd
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK
| | - Heidi E Jones
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Sean Davis
- Departments of Biomedical Informatics and Medicine, University of Colorado Anschutz School of Medicine, Denver, CO, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- Istituto Europeo di Oncologia (IEO) IRCSS, Milan, Italy
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Levi Waldron
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA.
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA.
- Department CIBIO, University of Trento, Trento, Italy.
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Handley BL, Sokana O, Addo KK, Wagner J, Fookes M, Harding-Esch E, Marks M, Thomson NR, Doyle RM. Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment. Microb Genom 2024; 10. [PMID: 38739120 DOI: 10.1099/mgen.0.001234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Cutaneous ulcers are common in yaws-endemic areas. Although often attributed to 'Treponema pallidum subsp. pertenue' and Haemophilus ducreyi, quantitative PCR has highlighted a significant proportion of these ulcers are negative for both pathogens and are considered idiopathic. This is a retrospective analysis utilising existing 16S rRNA sequencing data from two independent yaws studies that took place in Ghana and the Solomon Islands. We characterized bacterial diversity in 38 samples to identify potential causative agents for idiopathic cutaneous ulcers. We identified a diverse bacterial profile, including Arcanobacterium haemolyticum, Campylobacter concisus, Corynebacterium diphtheriae, Staphylococcus spp. and Streptococcus pyogenes, consistent with findings from previous cutaneous ulcer microbiome studies. No single bacterial species was universally present across all samples. The most prevalent bacterium, Campylobacter ureolyticus, appeared in 42% of samples, suggesting a multifactorial aetiology for cutaneous ulcers in yaws-endemic areas. This study emphasizes the need for a nuanced understanding of potential causative agents. The findings prompt further exploration into the intricate microbial interactions contributing to idiopathic yaw-like ulcers, guiding future research toward comprehensive diagnostic and therapeutic strategies.
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Affiliation(s)
- Becca L Handley
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Oliver Sokana
- Solomon Islands Ministry of Health, Honiara, Solomon Islands
| | - Kennedy Kwasi Addo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | | | - Emma Harding-Esch
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Marks
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, London, UK
- University College London, London, UK
| | | | - Ronan M Doyle
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
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13
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Havlena ZE, Hose LD, DuChene HR, Baker GM, Powell JD, Labrado AL, Brunner B, Jones DS. Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA. Geobiology 2024; 22:e12594. [PMID: 38700397 DOI: 10.1111/gbi.12594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/08/2023] [Accepted: 03/27/2024] [Indexed: 05/05/2024]
Abstract
Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ34SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.
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Affiliation(s)
- Zoë E Havlena
- Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Louise D Hose
- Department of Geological Sciences and Engineering, University of Nevada, Reno, Nevada, USA
| | | | | | - J Douglas Powell
- Humboldt-Toiyabe National Forest, Ely Ranger District, Nevada, USA
| | - Amanda L Labrado
- The Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Earth, Environmental and Resource Sciences, The University of Texas El Paso, El Paso, Texas, USA
| | - Benjamin Brunner
- Earth, Environmental and Resource Sciences, The University of Texas El Paso, El Paso, Texas, USA
| | - Daniel S Jones
- Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
- National Cave and Karst Research Institute, Carlsbad, New Mexico, USA
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14
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Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. bioRxiv 2024:2024.04.30.591865. [PMID: 38746196 PMCID: PMC11092579 DOI: 10.1101/2024.04.30.591865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
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15
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Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods 2024:10.1038/s41592-024-02262-1. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Affiliation(s)
- Daniel P Agustinho
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Vipin K Menon
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
- Senior research project manager, Human Genetics, Genentech, South San Francisco, CA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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16
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Battaglia TW, Mimpen IL, Traets JJH, van Hoeck A, Zeverijn LJ, Geurts BS, de Wit GF, Noë M, Hofland I, Vos JL, Cornelissen S, Alkemade M, Broeks A, Zuur CL, Cuppen E, Wessels L, van de Haar J, Voest E. A pan-cancer analysis of the microbiome in metastatic cancer. Cell 2024; 187:2324-2335.e19. [PMID: 38599211 DOI: 10.1016/j.cell.2024.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/30/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Microbial communities are resident to multiple niches of the human body and are important modulators of the host immune system and responses to anticancer therapies. Recent studies have shown that complex microbial communities are present within primary tumors. To investigate the presence and relevance of the microbiome in metastases, we integrated mapping and assembly-based metagenomics, genomics, transcriptomics, and clinical data of 4,160 metastatic tumor biopsies. We identified organ-specific tropisms of microbes, enrichments of anaerobic bacteria in hypoxic tumors, associations between microbial diversity and tumor-infiltrating neutrophils, and the association of Fusobacterium with resistance to immune checkpoint blockade (ICB) in lung cancer. Furthermore, longitudinal tumor sampling revealed temporal evolution of the microbial communities and identified bacteria depleted upon ICB. Together, we generated a pan-cancer resource of the metastatic tumor microbiome that may contribute to advancing treatment strategies.
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Affiliation(s)
- Thomas W Battaglia
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Iris L Mimpen
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Joleen J H Traets
- Division of Tumor Biology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Arne van Hoeck
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Department of Head and Neck Surgery and Oncology, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Laurien J Zeverijn
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Birgit S Geurts
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Gijs F de Wit
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Michaël Noë
- Department of Pathology, Antoni van Leeuwenhoek/the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ingrid Hofland
- Core Facility Molecular Pathology & Biobanking, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Joris L Vos
- Division of Tumor Biology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sten Cornelissen
- Core Facility Molecular Pathology & Biobanking, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Maartje Alkemade
- Core Facility Molecular Pathology & Biobanking, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Charlotte L Zuur
- Division of Tumor Biology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Department of Head and Neck Surgery and Oncology, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584CX, the Netherlands; Hartwig Medical Foundation, Science Park, Amsterdam 1098XH, the Netherlands
| | - Lodewyk Wessels
- Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft 2628 CD, the Netherlands
| | - Joris van de Haar
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Emile Voest
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands.
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17
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Older CE, Rodrigues Hoffmann A. Considerations for performing companion animal skin microbiome studies. Vet Dermatol 2024. [PMID: 38654617 DOI: 10.1111/vde.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/16/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.
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Affiliation(s)
- Caitlin E Older
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Aline Rodrigues Hoffmann
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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Ren M, Pan H, Zhou X, Yu M, Ji F. Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease. Sci Rep 2024; 14:9124. [PMID: 38643212 PMCID: PMC11032335 DOI: 10.1038/s41598-024-59605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 04/12/2024] [Indexed: 04/22/2024] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.
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Affiliation(s)
- Mengting Ren
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 158 Shangtang Road, Hangzhou, 310014, Zhejiang, China
| | - Hanghai Pan
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 158 Shangtang Road, Hangzhou, 310014, Zhejiang, China
| | - Xinxin Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Mosang Yu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
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Copeland DC, Ricigliano VA, Mott BM, Kortenkamp OL, Erickson RJ, Gorrochategui-Ortega J, Anderson KE. A longitudinal study of queen health in honey bees reveals tissue specific response to seasonal changes and pathogen pressure. Sci Rep 2024; 14:8963. [PMID: 38637564 PMCID: PMC11026438 DOI: 10.1038/s41598-024-58883-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
The health of honey bee queens is crucial for colony success, particularly during stressful periods like overwintering. To accompany a previous longitudinal study of colony and worker health, we explored niche-specific gut microbiota, host gene expression, and pathogen prevalence in honey bee queens overwintering in a warm southern climate. We found differential gene expression and bacterial abundance with respect to various pathogens throughout the season. Biologically older queens had larger microbiotas, particularly enriched in Bombella and Bifidobacterium. Both Deformed Wing Virus A and B subtypes were highest in the fat body tissue in January, correlating with colony Varroa levels, and Deformed Wing Virus titers in workers. High viral titers in queens were associated with decreased vitellogenin expression, suggesting a potential trade-off between immune function and reproductive capacity. Additionally, we found a complex and dynamic relationship between these viral loads and immune gene expression, indicating a possible breakdown in the coordinated immune response as the season progressed. Our study also revealed a potential link between Nosema and Melissococcus plutonius infections in queens, demonstrating that seasonal opportunism is not confined to just workers. Overall, our findings highlight the intricate interplay between pathogens, metabolic state, and immune response in honey bee queens. Combined with worker and colony-level metrics from the same colonies, our findings illustrate the social aspect of queen health and resilience over the winter dearth.
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Affiliation(s)
- Duan C Copeland
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA.
| | - Vincent A Ricigliano
- USDA-ARS Honey Bee Breeding, Genetics, and Physiology Laboratory, Baton Rouge, LA, 70820, USA
| | - Brendon M Mott
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA
| | - Oliver L Kortenkamp
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Robert J Erickson
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA
| | - June Gorrochategui-Ortega
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940, Leioa, Spain
| | - Kirk E Anderson
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA.
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ, 85721, USA.
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Dean CJ, Peña-Mosca F, Ray T, Wehri TJ, Sharpe K, Antunes, Jr. AM, Doster E, Fernandes L, Calles VF, Bauman C, Godden S, Heins B, Pinedo P, Machado VS, Caixeta LS, Noyes NR. Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives. Appl Environ Microbiol 2024; 90:e0223423. [PMID: 38497641 PMCID: PMC11022539 DOI: 10.1128/aem.02234-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/04/2024] [Indexed: 03/19/2024] Open
Abstract
The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26). IMPORTANCE Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.
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Affiliation(s)
- C. J. Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - F. Peña-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. J. Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - K. Sharpe
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - A. M. Antunes, Jr.
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - E. Doster
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L. Fernandes
- Department of Veterinary Sciences, Texas Tech University, Lubbock, Texas, USA
| | - V. F. Calles
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - C. Bauman
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - S. Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B. Heins
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - P. Pinedo
- Department of Animal Science, Colorado State University, Fort Collins, Colorado, USA
| | - V. S. Machado
- Department of Veterinary Sciences, Texas Tech University, Lubbock, Texas, USA
| | - L. S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N. R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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21
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Chen H, Zhan M, Liu S, Balloux F, Wang H. Unraveling the potential of metagenomic next-generation sequencing in infectious disease diagnosis: Challenges and prospects. Sci Bull (Beijing) 2024:S2095-9273(24)00267-6. [PMID: 38670851 DOI: 10.1016/j.scib.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 04/28/2024]
Affiliation(s)
- Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Minghua Zhan
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Si Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
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22
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Zhang E, Wong SY, Czechowski P, Terauds A, Ray AE, Benaud N, Chelliah DS, Wilkins D, Montgomery K, Ferrari BC. Effects of increasing soil moisture on Antarctic desert microbial ecosystems. Conserv Biol 2024:e14268. [PMID: 38622950 DOI: 10.1111/cobi.14268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 04/17/2024]
Abstract
Overgeneralization and a lack of baseline data for microorganisms in high-latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind-driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10-12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long-term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally.
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Affiliation(s)
- Eden Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Sin Yin Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Czechowski
- Helmholtz Institute for Metabolic, Obesity and Vascular Research, Leipzig, Germany
| | - Aleks Terauds
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Angelique E Ray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Devan S Chelliah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
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23
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Coskun ÖK, Gomez-Saez GV, Beren M, Özcan D, Günay SD, Elkin V, Hoşgörmez H, Einsiedl F, Eisenreich W, Orsi WD. Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community. FEMS Microbiol Ecol 2024; 100:fiae062. [PMID: 38632042 DOI: 10.1093/femsec/fiae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Doğacan Özcan
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Suna D Günay
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Viktor Elkin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Hakan Hoşgörmez
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Florian Einsiedl
- Chair of Hydrogeology, School of Engineering and Design, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstraße, 85748 Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
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24
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Yu J, Zhang Y, Wells JCK, Wei Z, Bajaj-Elliott M, Nielsen DS, Fewtrell MS. A Stress Reduction Intervention for Lactating Mothers Alters Maternal Gut, Breast Milk, and Infant Gut Microbiomes: Data from a Randomized Controlled Trial. Nutrients 2024; 16:1074. [PMID: 38613107 PMCID: PMC11013067 DOI: 10.3390/nu16071074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND This secondary analysis of data from a randomized controlled trial (RCT) investigated how the maternal gut, breast milk, and infant gut microbiomes may contribute to the effects of a relaxation intervention, which reduced maternal stress and promoted infant weight gain. METHODS An RCT was undertaken in healthy Chinese primiparous mother-infant pairs (340/7-376/7gestation weeks). Mothers were randomly allocated to either the intervention group (IG, listening to relaxation meditation) or the control group (CG). Outcomes were the differences in microbiome composition and the diversity in the maternal gut, breast milk, and infant gut at 1 (baseline) and 8 weeks (post-intervention) between IG and CG, assessed using 16S rRNA gene amplicon sequencing of fecal and breastmilk samples. RESULTS In total, 38 mother-infant pairs were included in this analysis (IG = 19, CG = 19). The overall microbiome community structure in the maternal gut was significantly different between the IG and CG at 1 week, with the difference being more significant at 8 weeks (Bray-Curtis distance R2 = 0.04 vs. R2 = 0.13). Post-intervention, a significantly lower α-diversity was observed in IG breast milk (observed features: CG = 295 vs. IG = 255, p = 0.032); the Bifidobacterium genera presented a higher relative abundance. A significantly higher α-diversity was observed in IG infant gut (observed features: CG = 73 vs. IG = 113, p < 0.001). CONCLUSIONS The findings were consistent with the hypothesis that the microbiome might mediate observed relaxation intervention effects via gut-brain axis and entero-mammary pathways; but confirmation is required.
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Affiliation(s)
- Jinyue Yu
- Childhood Nutrition Research Group, Population, Policy & Practice Department, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK; (J.Y.); (J.C.K.W.)
| | - Yan Zhang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China;
| | - Jonathan C. K. Wells
- Childhood Nutrition Research Group, Population, Policy & Practice Department, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK; (J.Y.); (J.C.K.W.)
| | - Zhuang Wei
- Department of Child Healthcare, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China;
| | - Mona Bajaj-Elliott
- Infection, Immunity & Inflammation Department, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK;
| | | | - Mary S. Fewtrell
- Childhood Nutrition Research Group, Population, Policy & Practice Department, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK; (J.Y.); (J.C.K.W.)
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25
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Gand M, Navickaite I, Bartsch LJ, Grützke J, Overballe-Petersen S, Rasmussen A, Otani S, Michelacci V, Matamoros BR, González-Zorn B, Brouwer MSM, Di Marcantonio L, Bloemen B, Vanneste K, Roosens NHCJ, AbuOun M, De Keersmaecker SCJ. Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes. Front Microbiol 2024; 15:1336532. [PMID: 38659981 PMCID: PMC11042533 DOI: 10.3389/fmicb.2024.1336532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024] Open
Abstract
Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.
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Affiliation(s)
- Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Indre Navickaite
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Lee-Julia Bartsch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Astrid Rasmussen
- Bacterial Reference Center, Statens Serum Institute, Copenhagen, Denmark
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Bruno González-Zorn
- Department of Animal Health, Complutense University of Madrid, Madrid, Spain
| | - Michael S. M. Brouwer
- Wageningen Bioveterinary Research Part of Wageningen University and Research, Lelystad, Netherlands
| | - Lisa Di Marcantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Bram Bloemen
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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26
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Odendaal J, Black N, Bennett PR, Brosens J, Quenby S, MacIntyre DA. The endometrial microbiota and early pregnancy loss. Hum Reprod 2024; 39:638-646. [PMID: 38195891 PMCID: PMC10988105 DOI: 10.1093/humrep/dead274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
The human endometrium is a dynamic entity that plays a pivotal role in mediating the complex interplay between the mother and developing embryo. Endometrial disruption can lead to pregnancy loss, impacting both maternal physical and psychological health. Recent research suggests that the endometrial microbiota may play a role in this, although the exact mechanisms are still being explored, aided by recent technological advancements and our growing understanding of host immune responses. Suboptimal or dysbiotic vaginal microbiota, characterized by increased microbial diversity and reduced Lactobacillus dominance, has been associated with various adverse reproductive events, including miscarriage. However, the mechanisms linking the lower reproductive tract microbiota with pregnancy loss remain unclear. Recent observational studies implicate a potential microbial continuum between the vaginal and endometrial niche in patients with pregnancy loss; however, transcervical sampling of the low biomass endometrium is highly prone to cross-contamination, which is often not controlled for. In this review, we explore emerging evidence supporting the theory that a dysbiotic endometrial microbiota may modulate key inflammatory pathways required for successful embryo implantation and pregnancy development. We also highlight that a greater understanding of the endometrial microbiota, its relationship with the local endometrial microenvironment, and potential interventions remain a focus for future research.
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Affiliation(s)
- Joshua Odendaal
- Division of Biomedical Sciences, Clinical Sciences Research Laboratories, Warwick Medical School, Tommy's National Centre for Miscarriage Research, University of Warwick, Coventry, UK
- University Hospitals Coventry & Warwickshire, Coventry, UK
| | - Naomi Black
- Division of Biomedical Sciences, Clinical Sciences Research Laboratories, Warwick Medical School, Tommy's National Centre for Miscarriage Research, University of Warwick, Coventry, UK
- University Hospitals Coventry & Warwickshire, Coventry, UK
| | - Phillip R Bennett
- Tommy’s National Centre for Miscarriage Research, Imperial College London, London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jan Brosens
- Division of Biomedical Sciences, Clinical Sciences Research Laboratories, Warwick Medical School, Tommy's National Centre for Miscarriage Research, University of Warwick, Coventry, UK
- University Hospitals Coventry & Warwickshire, Coventry, UK
| | - Siobhan Quenby
- Division of Biomedical Sciences, Clinical Sciences Research Laboratories, Warwick Medical School, Tommy's National Centre for Miscarriage Research, University of Warwick, Coventry, UK
- University Hospitals Coventry & Warwickshire, Coventry, UK
| | - David A MacIntyre
- Tommy’s National Centre for Miscarriage Research, Imperial College London, London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
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27
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Tan L, Zhang D, Li YX, Li Y, Guo T, Sun Y, Li N, Feng C. Identification of intratumor bacteria-associated prognostic risk score in adrenocortical carcinoma. Microbiol Spectr 2024; 12:e0372723. [PMID: 38421176 PMCID: PMC10986527 DOI: 10.1128/spectrum.03727-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
A landmark study by Poore et al. showed intratumor bacteria (ITBs) playing a critical role in most cancers by reproduction of The Cancer Genome Atlas (TCGA) transcriptome data. A recent study by Salzberg et al. argued that ITBs, being overstated as a methodology by Poore et al., were problematic. We previously reported that ITBs were prognostic in adrenocortical carcinoma (ACC), a highly aggressive rare disease using data by Poore et al., and here, we aimed to answer whether ITBs truly existed and were prognostic in ACC. ACC samples from our institutes underwent 16S rRNA sequencing [adrenocortical carcinoma blocks from Huashan Hospital and China Medical University (HS) cohort]. The ITB profile was compared to TCGA data processed by Poore et al. (TCGA-P) and TCGA data processed by Salzberg et al. (TCGA-S), respectively. The primary outcome was overall survival (OS). A total of 26 ACC cases (HS cohort) and 10 paraffin controls were sequenced. The TCGA cohort encompassed 77 cases. Two and four amid the top 10 abundant genera in HS cohort were not detected in TCGA-P and TCGA-S, respectively. Neither was alpha or beta diversity associated with survival nor could ACC be subtyped by ITB signature in the HS cohort. Notably, a five-genera ITB risk score (Corynebacterium, Mycoplasma, Achromobacter, Anaerococcus, and Streptococcus) for OS trained in the HS cohort was validated in both TCGA-P and TCGA-S cohorts and was independently prognostic. Whereas ITB signature on the whole may not be associated with ACC subtypes, certain ITB features are associated with prognosis, and a risk score could be generated and validated externally. IMPORTANCE In this report, we looked at the role of ITBs in ACC in patients with different race and sequencing platforms. We found a five-genera ITB risk score consistently predicted overall survival in all cohorts. We conclude that certain ITB features are universally pathogenic to ACC.
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Affiliation(s)
- Linyi Tan
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dengwei Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
| | - Yong-xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
| | - Yuqing Li
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ting Guo
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yang Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ning Li
- Department of Urology, Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chenchen Feng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
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28
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Wesseltoft JB, Danielsen CD, Andersen AM, de Jonge N, Olsen A, Rohde PD, Kristensen TN. Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome. Sci Rep 2024; 14:7799. [PMID: 38565609 PMCID: PMC10987527 DOI: 10.1038/s41598-024-58500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024] Open
Abstract
It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. Here we used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. Our hypothesis was that flies constitutively enriched with a 'Young microbiome' would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an 'Old microbiome'. Three major take home messages came out of our study: (1) the gut microbiomes of young and old flies differ markedly; (2) feeding flies with Young and Old microbiomes altered the microbiome of recipient flies and (3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient flies, contradicting our working hypothesis. Combined, these results provide novel insight into the interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics can be complex and unpredictable.
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Affiliation(s)
| | | | | | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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29
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Kelly LA, Yost CK, Cooke SJ. Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research. J Fish Biol 2024; 104:912-919. [PMID: 38226503 DOI: 10.1111/jfb.15650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.
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Affiliation(s)
- Lisa A Kelly
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Christopher K Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
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30
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Dai JH, Tan XR, Qiao H, Liu N. Emerging clinical relevance of microbiome in cancer: promising biomarkers and therapeutic targets. Protein Cell 2024; 15:239-260. [PMID: 37946397 PMCID: PMC10984626 DOI: 10.1093/procel/pwad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
The profound influence of microbiota in cancer initiation and progression has been under the spotlight for years, leading to numerous researches on cancer microbiome entering clinical evaluation. As promising biomarkers and therapeutic targets, the critical involvement of microbiota in cancer clinical practice has been increasingly appreciated. Here, recent progress in this field is reviewed. We describe the potential of tumor-associated microbiota as effective diagnostic and prognostic biomarkers, respectively. In addition, we highlight the relationship between microbiota and the therapeutic efficacy, toxicity, or side effects of commonly utilized treatments for cancer, including chemotherapy, radiotherapy, and immunotherapy. Given that microbial factors influence the cancer treatment outcome, we further summarize some dominating microbial interventions and discuss the hidden risks of these strategies. This review aims to provide an overview of the applications and advancements of microbes in cancer clinical relevance.
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Affiliation(s)
- Jia-Hao Dai
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510050, China
| | - Xi-Rong Tan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510050, China
| | - Han Qiao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510050, China
| | - Na Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510050, China
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31
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Welsh BL, Eisenhofer R. The prevalence of controls in phyllosphere microbiome research: a methodological review. New Phytol 2024; 242:23-29. [PMID: 38339825 DOI: 10.1111/nph.19573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research.
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Affiliation(s)
- Brady L Welsh
- School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, 1353, Denmark
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32
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Gancz AS, Wright SL, Weyrich LS. Ancient human dental calculus metadata collection and sampling strategies: Recommendations for best practices. Am J Biol Anthropol 2024; 183:e24871. [PMID: 37994571 DOI: 10.1002/ajpa.24871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVES Ancient human dental calculus is a unique, nonrenewable biological resource encapsulating key information about the diets, lifestyles, and health conditions of past individuals and populations. With compounding calls its destructive analysis, it is imperative to refine the ways in which the scientific community documents, samples, and analyzes dental calculus so as to maximize its utility to the public and scientific community. MATERIALS AND METHODS Our research team conducted an IRB-approved survey of dental calculus researchers with diverse academic backgrounds, research foci, and analytical specializations. RESULTS This survey reveals variation in how metadata is collected and utilized across different subdisciplines and highlights how these differences have profound implications for dental calculus research. Moreover, the survey suggests the need for more communication between those who excavate, curate, and analyze biomolecular data from dental calculus. DISCUSSION Challenges in cross-disciplinary communication limit researchers' ability to effectively utilize samples in rigorous and reproducible ways. Specifically, the lack of standardized skeletal and dental metadata recording and contamination avoidance procedures hinder downstream anthropological applications, as well as the pursuit of broader paleodemographic and paleoepidemiological inquiries that rely on more complete information about the individuals sampled. To provide a path forward toward more ethical and standardized dental calculus sampling and documentation approaches, we review the current methods by which skeletal and dental metadata are recorded. We also describe trends in sampling and contamination-control approaches. Finally, we use that information to suggest new guidelines for ancient dental calculus documentation and sampling strategies that will improve research practices in the future.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sterling L Wright
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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33
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Sakamoto M, Tanaka H, Enomoto S, Takeuchi H, Nishioka M, Tanaka K, Takayama E, Maezawa T, Kondo E, Ikeda T. The efficacy of vaginal treatment for non-Lactobacillus dominant endometrial microbiota-A case-control study. J Obstet Gynaecol Res 2024; 50:604-610. [PMID: 38308457 DOI: 10.1111/jog.15897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
AIM Reduced Lactobacillus occupancy in the uterine microflora has been associated with implantation failure. This study aimed to evaluate a treatment for improving the uterine microflora. METHODS This study included patients diagnosed with repeated implantation failure-defined as failure to achieve pregnancy after two or more transfers of viable embryos-who were classified as non-Lactobacillus dominant. Treatment A comprised oral administration of antibiotics for 1 week, followed by oral probiotic butyrate tablets (3 g/day) for approximately 30 days. Treatment B comprised a 1-week course of oral (750 mg/day) and vaginal (250 mg/day) metronidazole, followed by a 1-week intravaginal administration of probiotic capsules (1 capsule/day) and continued oral administration of probiotics (1 capsule/day). Both treatments were compared in terms of efficacy in improving vaginal flora. Improvement was defined as Lactobacillus occupancy >90% or an increase in Lactobacillus occupancy >20%. RESULTS Seven (41.2%) of 17 patients in the Treatment A group improved in response to the treatment. Contrastingly, 9 (90.0%) of 10 patients improved in the Treatment B group (p = 0.0127). Following treatment, Lactobacillus occupancy in the Treatment B group (62.9% ± 12.7%) was significantly higher than that in the Treatment A group (5.7% ± 9.8%) (p = 0.0242). CONCLUSIONS This study demonstrates the effectiveness of combining antibiotics and probiotics in vaginal formulations for treating abnormal uterine microflora. However, its potential impact on in vitro fertilization outcomes remains unclear and warrants further investigation through larger, more comprehensive studies.
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Affiliation(s)
- Mito Sakamoto
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Hiroaki Tanaka
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Sayako Enomoto
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Hiroki Takeuchi
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Mikiko Nishioka
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Kayo Tanaka
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Erina Takayama
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Tadashi Maezawa
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Eiji Kondo
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
| | - Tomoaki Ikeda
- Department of Obstetrics and Gynecology, Mie University School of Medicine, Mie, Japan
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34
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Bano Y, Shrivastava A, Shukla P, Chaudhary AA, Khan SUD, Khan S. The implication of microbiome in lungs cancer: mechanisms and strategies of cancer growth, diagnosis and therapy. Crit Rev Microbiol 2024:1-25. [PMID: 38556797 DOI: 10.1080/1040841x.2024.2324864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Available evidence illustrates that microbiome is a promising target for the study of growth, diagnosis and therapy of various types of cancer. Lung cancer is a leading cause of cancer death worldwide. The relationship of microbiota and their products with diverse pathologic conditions has been getting large attention. The novel research suggests that the microbiome plays an important role in the growth and progression of lung cancer. The lung microbiome plays a crucial role in maintaining mucosal immunity and synchronizing the stability between tolerance and inflammation. Alteration in microbiome is identified as a critical player in the progression of lung cancer and negatively impacts the patient. Studies suggest that healthy microbiome is essential for effective therapy. Various clinical trials and research are focusing on enhancing the treatment efficacy by altering the microbiome. The regulation of microbiota will provide innovative and promising treatment strategies for the maintenance of host homeostasis and the prevention of lung cancer in lung cancer patients. In the current review article, we presented the latest progress about the involvement of microbiome in the growth and diagnosis of lung cancer. Furthermore, we also assessed the therapeutic status of the microbiome for the management and treatment of lung cancer.
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Affiliation(s)
- Yasmin Bano
- Department of Biotechnology, College of Life Sciences, Cancer Hospital and research Institute, Gwalior, India
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, India
| | - Abhinav Shrivastava
- Department of Biotechnology, College of Life Sciences, Cancer Hospital and research Institute, Gwalior, India
| | - Piyush Shukla
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, India
- Laboratory of Natural Products, Department of Rural Technology and Social Development, Guru Ghasidas University, Bilaspur, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Shahanavaj Khan
- Department of Medical Lab Technology, Indian Institute of Health Technology (IIHT), Deoband, Saharanpur, UP, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, Australia
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35
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Blanco-Míguez A, Carloni S, Cardenas C, Dioguardi CC, Lambroia L, Capretti G, Nappo G, Fugazza A, Capogreco A, Armanini F, Asnicar F, Dubois L, Golzato D, Manghi P, Pinto F, Scuderi C, Casari E, Montorsi M, Anderloni A, Rescigno M, Repici A, Zerbi A, Peano C, Tamburini S, Rusconi R, Segata N. Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer. NPJ Biofilms Microbiomes 2024; 10:35. [PMID: 38555334 PMCID: PMC10981703 DOI: 10.1038/s41522-024-00506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Malignant bile duct obstruction is typically treated by biliary stenting, which however increases the risk of bacterial infections. Here, we analyzed the microbial content of the biliary stents from 56 patients finding widespread microbial colonization. Seventeen of 36 prevalent stent species are common oral microbiome members, associate with disease conditions when present in the gut, and include dozens of biofilm- and antimicrobial resistance-related genes. This work provides an overview of the microbial communities populating the stents.
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Affiliation(s)
| | - Sara Carloni
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | | | - Carola Conca Dioguardi
- Institute of Genetics and Biomedical Research, UoS of Milan, National Research Council, Rozzano, Milan, Italy
| | - Luca Lambroia
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giovanni Capretti
- Department of Pancreatic Surgery, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Gennaro Nappo
- Department of Pancreatic Surgery, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Alessandro Fugazza
- Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Antonio Capogreco
- Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | | | | | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Cristina Scuderi
- Microbiology and Virology Unit, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Erminia Casari
- Microbiology and Virology Unit, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Marco Montorsi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Andrea Anderloni
- Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Maria Rescigno
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Alessandro Repici
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Alessandro Zerbi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Department of Pancreatic Surgery, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Clelia Peano
- Institute of Genetics and Biomedical Research, UoS of Milan, National Research Council, Rozzano, Milan, Italy
- Human Technopole, Milan, Italy
| | | | - Roberto Rusconi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy.
- IRCCS Humanitas Research Hospital, Rozzano, Italy.
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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36
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Li M, Jin M, Zhao L, Yu D, Li Y, Shi L, Zhou B, Liu L, Cao Y, Cai K, Fan J, Nie X, Zhang T, Liu H. Tumor-associated microbiota in colorectal cancer with vascular tumor thrombus and neural invasion and association with clinical prognosis. Acta Biochim Biophys Sin (Shanghai) 2024; 56:366-378. [PMID: 37905339 PMCID: PMC10984857 DOI: 10.3724/abbs.2023255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Neural invasion (NI) and vascular tumor thrombus (VT) are associated with poor prognosis in patients with colorectal cancer (CRC). In this study, we apply 16S rRNA amplicon sequencing to tumor tissues and adjacent normal tissues in patients with CRC to determine the microbial differences. A discovery cohort, including 30 patients with NI, 23 with VT, and 35 with double-negative CRC tissue, is utilized. Then, we analyze the relationship between the specific bacterial taxa and indicators of different dimensions in separate cohorts. In the discovery cohort, the diversity and composition of the gut microbiome distinctly differ between the tumor and nontumor tissues in the NI and VT groups. A high abundance of Cupriavidus is found to be related to a short survival time of NI CRC, while Herbaspirillum is a potential microbial biomarker predicting the prognosis of patients with CRC with NI or VT. Moreover, the abundance of Cupriavidus or Herbaspirillum is associated with some clinical patient characteristics and prognosis, respectively. In conclusion, this study is the first to comprehensively elaborate the differences in the gut microbiota of patients with CRC with different invasion statuses and to prove the relationship between some gut microbiota and clinical patient characteristics.
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Affiliation(s)
- Mingjie Li
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Min Jin
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Lei Zhao
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Dandan Yu
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Yan Li
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Linli Shi
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Bin Zhou
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Li Liu
- of Epidemiology and Biostatisticsthe Ministry of Education Key Lab of Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Yinghao Cao
- Department of Gastrointestinal SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Hubei Key Laboratory of Precision Radiation OncologyWuhan430022China
| | - Kailin Cai
- Department of Gastrointestinal SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Jun Fan
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Xiu Nie
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Tao Zhang
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Hongli Liu
- Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Institute of Radiation. OncologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
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Iyer V, Castro D, Malla B, Panda B, Rabson AR, Horowitz G, Heger N, Gupta K, Singer A, Norwitz ER. Culture-independent identification of bloodstream infections from whole blood: prospective evaluation in specimens of known infection status. J Clin Microbiol 2024; 62:e0149823. [PMID: 38315022 PMCID: PMC10935643 DOI: 10.1128/jcm.01498-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Sepsis caused by bloodstream infection (BSI) is a major healthcare burden and a leading cause of morbidity and mortality worldwide. Timely diagnosis is critical to optimize clinical outcome, as mortality rates rise every hour treatment is delayed. Blood culture remains the "gold standard" for diagnosis but is limited by its long turnaround time (1-7 days depending on the organism) and its potential to provide false-negative results due to interference by antimicrobial therapy or the presence of mixed (i.e., polymicrobial) infections. In this paper, we evaluated the performance of resistance and pathogen ID/BSI, a direct-from-specimen molecular assay. To reduce the false-positivity rate common with molecular methods, this assay isolates and detects genomic material only from viable microorganisms in the blood by incorporating a novel precursor step to selectively lyse host and non-viable microbial cells and remove cell-free genomic material prior to lysis and analysis of microbial cells. Here, we demonstrate that the assay is free of interference from host immune cells and common antimicrobial agents at elevated concentrations. We also demonstrate the accuracy of this technology in a prospective cohort pilot study of individuals with known sepsis/BSI status, including samples from both positive and negative individuals. IMPORTANCE Blood culture remains the "gold standard" for the diagnosis of sepsis/bloodstream infection (BSI) but has many limitations which may lead to a delay in appropriate and accurate treatment in patients. Molecular diagnostic methods have the potential for markedly improving the management of such patients through faster turnaround times and increased accuracy. But molecular diagnostic methods have not been widely adopted for the identification of BSIs. By incorporating a precursor step of selective lysis of host and non-viable microorganisms, our resistance and pathogen ID (RaPID)/BSI molecular assay addresses many limitations of blood culture and other molecular assay. The RaPID/BSI assay has an approximate turnaround time of 4 hours, thereby significantly reducing the time to appropriate and accurate diagnosis of causative microorganisms in such patients. The short turnaround time also allows for close to real-time tracking of pathogenic clearance of microorganisms from the blood of these patients or if a change of antimicrobial regimen is required. Thus, the RaPID/BSI molecular assay helps with optimization of antimicrobial stewardship; prompt and accurate diagnosis of sepsis/BSI could help target timely treatment and reduce mortality and morbidity in such patients.
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Affiliation(s)
- Vidya Iyer
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Castro
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Bipin Malla
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Britta Panda
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Arthur R. Rabson
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Gary Horowitz
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Nicholas Heger
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | | | - Alon Singer
- HelixBind Inc., Boxborough, Massachusetts, USA
| | - Errol R. Norwitz
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, Massachusetts, USA
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Yu B, Liu C, Proll SC, Manhardt E, Liang S, Srinivasan S, Swisher E, Fredricks DN. Identification of fallopian tube microbiota and its association with ovarian cancer. eLife 2024; 12:RP89830. [PMID: 38451065 PMCID: PMC10942644 DOI: 10.7554/elife.89830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Investigating the human fallopian tube (FT) microbiota has significant implications for understanding the pathogenesis of ovarian cancer (OC). In this large prospective study, we collected swabs intraoperatively from the FT and other surgical sites as controls to profile the microbiota in the FT and to assess its relationship with OC. Eighty-one OC and 106 non-cancer patients were enrolled and 1001 swabs were processed for 16S rRNA gene PCR and sequencing. We identified 84 bacterial species that may represent the FT microbiota and found a clear shift in the microbiota of the OC patients when compared to the non-cancer patients. Of the top 20 species that were most prevalent in the FT of OC patients, 60% were bacteria that predominantly reside in the gastrointestinal tract, while 30% normally reside in the mouth. Serous carcinoma had higher prevalence of almost all 84 FT bacterial species compared to the other OC subtypes. The clear shift in the FT microbiota in OC patients establishes the scientific foundation for future investigation into the role of these bacteria in the pathogenesis of OC.
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Affiliation(s)
- Bo Yu
- Department of Obstetrics and GynecologyStanfordUnited States
- Stanford Maternal & Child Health Research Institute, Stanford University School of MedicineStanfordUnited States
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Sean C Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Enna Manhardt
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - Shuying Liang
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Elizabeth Swisher
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
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Fu Y, Gu J, Chen LJ, Xiong M, Zhao J, Xiao X, Zhou J, Li Z, Li Y. A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections. Microbiol Spectr 2024; 12:e0331723. [PMID: 38294222 PMCID: PMC10913467 DOI: 10.1128/spectrum.03317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Central nervous system (CNS) infections are a leading cause of death in patients. Nanopore-targeted sequencing (NTS) has begun to be used for pathogenic microbial detection. This study aims to evaluate the ability of NTS in the detection of pathogens in cerebrospinal fluid (CSF) through a prospective study. Fifty CSF specimens collected from 50 patients with suspected CNS infections went through three methods including NTS, metagenomic next-generation sequencing (mNGS), and microbial culture in parallel. When there was an inconsistency between NTS results and the results of the mNGS, the 16S rDNA gene was amplified followed by Sanger sequencing to further verify pathogens detected by NTS. Among 50 CSF specimens, 76% were NTS-positive, which is lower than mNGS (94.0%), yet higher than microbial culture (16.0%). The overall validation rate, diagnostic accordance rate (DAR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NTS were 86.7%, 50.0%, 71.0%, 15.8%, 57.9%, and 25.0%, respectively. In the CSF total nucleated cell (TNC) number ≤10 cells/µL, DAR, specificity, and PPV were 20%, 11.1%, and 11.1%, whereas in that with CSF TNC number >10 cells/µL, DAR, sensitivity, specificity, PPV, and NPV were 57.5%, 70.0%, 20.0%, 72.4%, and 18.2%, respectively. Although NTS has a higher microbial detection rate than microbial culture, it should combine CSF TNC result to evaluate the value of NTS for the diagnosis of CNS infections. IMPORTANCE This study aims to prospectively evaluate the ability of nanopore-targeted sequencing (NTS) in the detection of pathogens in cerebrospinal fluid (CSF). It was the first time combining mNGS and microbial culture to verify the NTS-positive results also using 16S rDNA amplification with Sanger sequencing. Although microbial culture was thought to be the gold standard for pathogens detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing central nervous system (CNS) infection. NTS should be recommended to be used in CSF for diagnosing CNS infection. When evaluating the value of NTS for diagnosis of CNS infections, the results of CSF TNC should be combined, and NTS-positive result is observed to be more reliable in patients with CSF TNC level >10 cells/μL.
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Affiliation(s)
- Yu Fu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jihong Gu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang-Jun Chen
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyuan Xiong
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jin Zhao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao Xiao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junying Zhou
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yirong Li
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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Sun X, Huang D, Huang Y, Häggblom M, Soleimani M, Li J, Chen Z, Chen Z, Gao P, Li B, Sun W. Microbial-mediated oxidative dissolution of orpiment and realgar in circumneutral aquatic environments. Water Res 2024; 251:121163. [PMID: 38266438 DOI: 10.1016/j.watres.2024.121163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Arsenic (As) is a toxic metalloid that causes severe environmental contamination worldwide. Upon exposure to aqueous phases, the As-bearing minerals, such as orpiment (As2S3) and realgar (As4S4), undergo oxidative dissolution, in which biotic and abiotic activities both contributed significant roles. Consequently, the dissolved As and S are rapidly discharged through water transportation to broader regions and contaminate surrounding areas, especially in aquatic environments. Despite both orpiment and realgar are frequently encountered in carbonate-hosted neutral environments, the microbial-mediated oxidative dissolution of these minerals, however, have been primarily investigated under acidic conditions. Therefore, the current study aimed to elucidate microbial-mediated oxidative dissolution under neutral aquatic conditions. The current study demonstrated that the dissolution of orpiment and realgar is synergistically regulated by abiotic (i.e., specific surface area (SSA) of the mineral) and biotic (i.e., microbial oxidation) factors. The initial dissolution of As(III) and S2- from minerals is abiotically impacted by SSA, while the microbial oxidation of As(III) and S2- accelerated the overall dissolution rates of orpiment and realgar. In As-contaminated environments, members of Thiobacillus and Rhizobium were identified as the major populations that mediated oxidative dissolution of orpiment and realgar by DNA-stable isotope probing. This study provides novel insights regarding the microbial-mediated oxidative dissolution process of orpiment and realgar under neutral conditions.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Yuqing Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Max Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Jiayi Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Zhenyu Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; School of Environment, Henan Normal University, Xinxiang 453007, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Academy of Sciences, Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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Balboni A, Franzo G, Bano L, Urbani L, Segatore S, Rizzardi A, Cordioli B, Cornaggia M, Terrusi A, Vasylyeva K, Dondi F, Battilani M. No viable bacterial communities reside in the urinary bladder of cats with feline idiopathic cystitis. Res Vet Sci 2024; 168:105137. [PMID: 38181480 DOI: 10.1016/j.rvsc.2024.105137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Urinary microbial diversities have been reported in humans according to sex, age and clinical status, including painful bladder syndrome/interstitial cystitis (PBS/IC). To date, the role of the urinary microbiome in the pathogenesis of PBS/IC is debated. Feline idiopathic cystitis (FIC) is a chronic lower urinary tract disorder affecting cats with similarities to PBS/IC in women and represents an important problem in veterinary medicine as its aetiology is currently unknown. In this study, the presence of a bacterial community residing in the urinary bladder of cats with a diagnosis of FIC was investigated. Nineteen cats with clinical signs and history of FIC and without growing bacteria in standard urine culture were included and urine collected with ultrasound-guided cystocentesis. Bacterial community was investigated using a culture-dependent approach consisted of expanded quantitative urine culture techniques and a culture-independent approach consisted of 16S rRNA NGS. Several methodological practices were adopted to both avoid and detect any contamination or bias introduced by means of urine collection and processing which could be relevant due to the low microbial biomass environment of the bladder and urinary tract, including negative controls analysis. All the cats included showed no growing bacteria in the urine analysed. Although few reads were originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and negative controls, and no taxa were confidently classified as non-contaminant. The results obtained suggest the absence of viable bacteria and of bacterial DNA of urinary origin in the urinary bladder of cats with FIC.
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Affiliation(s)
- Andrea Balboni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Luca Bano
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Lorenza Urbani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Sofia Segatore
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Alessia Rizzardi
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Benedetta Cordioli
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Matteo Cornaggia
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Alessia Terrusi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Kateryna Vasylyeva
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Mara Battilani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
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Street TL, Sanderson ND, Barker L, Kavanagh J, Cole K, Llewelyn M, Eyre DW. Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing. Microb Genom 2024; 10:001208. [PMID: 38529900 PMCID: PMC10995632 DOI: 10.1099/mgen.0.001208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/10/2024] [Indexed: 03/27/2024] Open
Abstract
Multi-drug-resistant Neisseria gonorrhoeae infection is a significant public health risk. Rapidly detecting N. gonorrhoeae and antimicrobial-resistant (AMR) determinants by metagenomic sequencing of urine is possible, although high levels of host DNA and overgrowth of contaminating species hamper sequencing and limit N. gonorrhoeae genome coverage. We performed Nanopore sequencing of nucleic acid amplification test-positive urine samples and culture-positive urethral swabs with and without probe-based target enrichment, using a custom SureSelect panel, to investigate whether selective enrichment of N. gonorrhoeae DNA improves detection of both species and AMR determinants. Probes were designed to cover the entire N. gonorrhoeae genome, with tenfold enrichment of probes covering selected AMR determinants. Multiplexing was tested in a subset of samples. The proportion of sequence bases classified as N. gonorrhoeae increased in all samples after enrichment, from a median (IQR) of 0.05 % (0.01-0.1 %) to 76 % (42-82 %), giving a corresponding median improvement in fold genome coverage of 365 times (112-720). Over 20-fold coverage, required for robust AMR determinant detection, was achieved in 13/15(87 %) samples, compared to 2/15(13 %) without enrichment. The four samples multiplexed together also achieved >20-fold genome coverage. Coverage of AMR determinants was sufficient to predict resistance conferred by changes in chromosomal genes, where present, and genome coverage also enabled phylogenetic relationships to be reconstructed. Probe-based target enrichment can improve N. gonorrhoeae genome coverage when sequencing DNA extracts directly from urine or urethral swabs, allowing for detection of AMR determinants. Additionally, multiplexing prior to enrichment provided enough genome coverage for AMR detection and reduces the costs associated with this method.
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Affiliation(s)
- Teresa L. Street
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicholas D. Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kevin Cole
- Department of Microbiology and Infection, University Hospitals Sussex NHS Trust, Brighton, UK
| | - The GonFast Investigators Group
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Department of Microbiology and Infection, University Hospitals Sussex NHS Trust, Brighton, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Martin Llewelyn
- Department of Microbiology and Infection, University Hospitals Sussex NHS Trust, Brighton, UK
| | - David W. Eyre
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Pust MM, Rocha Castellanos DM, Rzasa K, Dame A, Pishchany G, Assawasirisin C, Liss A, Fernandez-Del Castillo C, Xavier RJ. Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm. Gut 2024:gutjnl-2023-331012. [PMID: 38429112 DOI: 10.1136/gutjnl-2023-331012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVE This study aims to validate the existence of a microbiome within intraductal papillary mucinous neoplasm (IPMN) that can be differentiated from the taxonomically diverse DNA background of next-generation sequencing procedures. DESIGN We generated 16S rRNA amplicon sequencing data to analyse 338 cyst fluid samples from 190 patients and 19 negative controls, the latter collected directly from sterile syringes in the operating room. A subset of samples (n=20) and blanks (n=5) were spiked with known concentrations of bacterial cells alien to the human microbiome to infer absolute abundances of microbial traces. All cyst fluid samples were obtained intraoperatively and included IPMNs with various degrees of dysplasia as well as other cystic neoplasms. Follow-up culturing experiments were conducted to assess bacterial growth for microbiologically significant signals. RESULTS Microbiome signatures of cyst fluid samples were inseparable from those of negative controls, with no difference in taxonomic diversity, and microbial community composition. In a patient subgroup that had recently undergone invasive procedures, a bacterial signal was evident. This outlier signal was not characterised by higher taxonomic diversity but by an increased dominance index of a gut-associated microbe, leading to lower taxonomic evenness compared with the background signal. CONCLUSION The 'microbiome' of IPMNs and other pancreatic cystic neoplasms does not deviate from the background signature of negative controls, supporting the concept of a sterile environment. Outlier signals may appear in a small fraction of patients following recent invasive endoscopic procedures. No associations between microbial patterns and clinical or cyst parameters were apparent.
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Affiliation(s)
- Marie-Madlen Pust
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Kara Rzasa
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrea Dame
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gleb Pishchany
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charnwit Assawasirisin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
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44
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Sweeney CJ, Kaushik R, Bottoms M. Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome. Integr Environ Assess Manag 2024; 20:337-358. [PMID: 37452668 DOI: 10.1002/ieam.4812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.
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Affiliation(s)
- Christopher J Sweeney
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Rishabh Kaushik
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Melanie Bottoms
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
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Lin BW, Hong JC, Jiang ZJ, Zhang WQ, Fan QC, Yao XP. Performance of metagenomic next-generation sequencing in cerebrospinal fluid for diagnosis of tuberculous meningitis. J Med Microbiol 2024; 73. [PMID: 38506717 DOI: 10.1099/jmm.0.001818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Purpose. Metagenomic next-generation sequencing (mNGS) has been widely used in the diagnosis of infectious diseases, while its performance in diagnosis of tuberculous meningitis (TBM) is incompletely characterized. The aim of this study was to assess the performance of mNGS in the diagnosis of TBM, and illustrate the sensitivity and specificity of different methods.Methods. We retrospectively recruited TBM patients between January 2021 and March 2023 to evaluate the performance of mNGS on cerebrospinal fluid (CSF) samples, in comparison with conventional microbiological testing, including culturing of Mycobacterium tuberculosis (MTB), acid-fast bacillus (AFB) stain, reverse transcription PCR and Xpert MTB/RIF.Results. Of the 40 enrolled, 34 participants were diagnosed with TBM, including 15(44.12 %) definite and 19(55.88 %) clinical diagnosis based upon clinical manifestations, CSF parameters, brain imaging, pathogen evidence and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MTBC) in 11 CSF samples. In patients with definite TBM, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of mNGS were 78.57, 100, 100, 66.67 and 85 %, respectively. Compared to conventional diagnostic methods, the sensitivity of mNGS (78.57 %) was higher than AFB (0 %), culturing (0 %), RT-PCR (60 %) and Xpert MTB/RIF (14.29 %).Conclusions. Our study indicates that mNGS of CSF exhibited an overall improved sensitivity over conventional diagnostic methods for TBM and can be considered a front-line CSF test.
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Affiliation(s)
- Bi-Wei Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
| | - Jian-Chen Hong
- Department of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Zai-Jie Jiang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
| | - Wei-Qing Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Qi-Chao Fan
- Department of Infectious Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Xiang-Ping Yao
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, PR China
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Corral-Vazquez C, Blanco J, Sarrate Z, Anton E. Unraveling the Intricacies of the Seminal Microbiome and Its Impact on Human Fertility. Biology (Basel) 2024; 13:150. [PMID: 38534419 DOI: 10.3390/biology13030150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024]
Abstract
Although the microbial communities from seminal fluid were an unexplored field some decades ago, their characteristics and potential roles are gradually coming to light. Therefore, a complex and specific microbiome population with commensal niches and fluctuating species has started to be revealed. In fact, certain clusters of bacteria have been associated with fertility and health, while the outgrowth of several species is potentially correlated with infertility indicators. This constitutes a compelling reason for outlining the external elements that may induce changes in the seminal microbiome composition, like lifestyle factors, gut microbiota, pathologies, prebiotics, and probiotics. In this review, we summarize the main findings about seminal microbiome, its origins and composition, its relationship with fertility, health, and influence factors, while reminding readers of the limitations and advantages introduced from technical variabilities during the experimental procedures.
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Affiliation(s)
- Celia Corral-Vazquez
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Joan Blanco
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Zaida Sarrate
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Ester Anton
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular (Facultat de Biociències), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
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Fakhimi N, Torres MJ, Fernández E, Galván A, Dubini A, González-Ballester D. Chlamydomonas reinhardtii and Microbacterium forte sp. nov., a mutualistic association that favors sustainable hydrogen production. Sci Total Environ 2024; 913:169559. [PMID: 38159768 DOI: 10.1016/j.scitotenv.2023.169559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
A naturally occurring multispecies bacterial community composed of Bacillus cereus and two novel bacteria (Microbacterium forte sp. nov. and Stenotrophomonas goyi sp. nov.) has been identified from a contaminated culture of the microalga Chlamydomonas reinhardtii. When incubated in mannitol- and yeast extract-containing medium, this bacterial community can promote and sustain algal hydrogen production up to 313 mL H2·L-1 for 17 days and 163.5 mL H2·L-1 for 25 days in high-cell (76.7 μg·mL-1 of initial chlorophyll) and low-cell density (10 μg·mL-1 of initial chlorophyll) algal cultures, respectively. In low-cell density algal cultures, hydrogen production was compatible with algal growth (reaching up to 60 μg·mL-1 of chlorophyll). Among the bacterial community, M. forte sp. nov. was the sole responsible for the improvement in hydrogen production. However, algal growth was not observed in the Chlamydomonas-M. forte sp. nov. consortium during hydrogen-producing conditions (hypoxia), suggesting that the presence of B. cereus and S. goyi sp. nov. could be crucial to support the algal growth during hypoxia. Still, under non‑hydrogen producing conditions (aerobiosis) the Chlamydomonas-M. forte sp. nov. consortium allowed algal growth (up to 40 μg·mL-1 of chlorophyll) and long-term algal viability (>45 days). The genome sequence and growth tests of M. forte sp. nov. have revealed that this bacterium is auxotroph for biotin and thiamine and unable to use sulfate as sulfur source; it requires S-reduced forms such as cysteine and methionine. Cocultures of Chlamydomonas reinhardtii and M. forte sp. nov. established a mutualistic association: the alga complemented the nutrient deficiencies of the bacterium, while the bacterium released ammonium (0.19 mM·day-1) and acetic acid (0.15 mM·day-1) for the alga. This work offers a promising avenue for photohydrogen production concomitant with algal biomass generation using nutrients not suitable for mixotrophic algal growth.
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Affiliation(s)
- Neda Fakhimi
- Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain; Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Stanford, CA, 94305, United States of America.
| | - María Jesus Torres
- Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain.
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain.
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain.
| | - Alexandra Dubini
- Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain.
| | - David González-Ballester
- Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain.
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Xin Q, Saborimanesh N, Ridenour C, Farooqi H. Fate, behaviour and microbial response of diluted bitumen and conventional crude spills in a simulated warm freshwater environment. Environ Pollut 2024; 343:123224. [PMID: 38159633 DOI: 10.1016/j.envpol.2023.123224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Diluted bitumen (DB), one of the most transported unconventional crude oils in Canada's pipelines, raises public concerns due to its potential spillage into freshwater environments. This study aimed to compare the fate and behaviour of DB versus conventional crude (CC) in a simulated warm freshwater environment. An equivalent of 10 L of either DB or CC was spilled into 1200 L of North Saskatchewan River (NSR) water containing natural NSR sediment (2.4 kg) in a mesoscale spill tank and its fate and behaviour at air/water temperatures of 18 °C/24 °C were monitored for 56 days. Oil mass distribution analysis showed that 42.3 wt % of CC and 63.6 wt% of DB resided in the oil slicks at the end of 56-day tests, consisting mainly high molecular weight (HMW) compounds (i.e., resins and asphaltenes). The lost oil contained mainly low molecular weight (LMW) compounds (i.e., light saturates and some aromatics) into the atmosphere, water column, and sediment through collective weathering processes. Notably, weathered CC emulsified with water and remained floating until the end, while the weathered DB mat started to lose its buoyancy after 24 days under quiescent conditions and resurfaced once waves were applied. Analysis of the microbial communities of water pre- and post-spills revealed the replacement of indigenous microbial communities with hydrocarbon-degrading species. Exposure to CC reduced the microbial diversity by 12%, while exposure to DB increased the diversity by 10%. During the early stages of the spill (up to Day 21), most dominant species were positively correlated with the benzene, toluene, ethylbenzene, and xylenes (BTEX) content or polycyclic aromatic hydrocarbon (PAH) content of the water column, while the dominant species at the later stages (Days 21-56) of the spill were negatively correlated with BTEX or PAH content and positively correlated with the total organic carbon (TOC) content in waters.
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Affiliation(s)
- Qin Xin
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada.
| | - Nayereh Saborimanesh
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada
| | - Christine Ridenour
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada
| | - Hena Farooqi
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada
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Stuij TM, Cleary DFR, Rocha RJM, Polónia ARM, Silva DAM, Louvado A, de Voogd NJ, Gomes NCM. Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol Ecol 2024; 100:fiae022. [PMID: 38366951 PMCID: PMC10939426 DOI: 10.1093/femsec/fiae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
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Affiliation(s)
- Tamara M Stuij
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Rui J M Rocha
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Davide A M Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
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50
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Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas ME, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOC. Genomic attributes of airway commensal bacteria and mucosa. Commun Biol 2024; 7:171. [PMID: 38347162 PMCID: PMC10861553 DOI: 10.1038/s42003-024-05840-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.
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Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ulrike Löber
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Jonathan S Ish-Horowicz
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
| | - Claire N McBrien
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Colin Churchward
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jeremy C Parker
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Conor Burke
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Aisling McGowan
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Gwyneth A Davies
- Population Data Science and Health Data Research UK BREATHE Hub, Swansea University Medical School, Swansea University, Swansea, UK
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Keir E Lewis
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Julian M Hopkin
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Orla O'Carroll
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - John Faul
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Joy Creaser-Thomas
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Mark Andrews
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Robin Ghosal
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Stefan Piatek
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Theda U P Bartolomaeus
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Till Birkner
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Sarah Dwyer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena M Turek
- National Heart and Lung Institute, Imperial College London, London, UK
| | - A William Musk
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Jennie Hui
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Michael Hunter
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Alan James
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Marc-Emmanuel Dumas
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- U1283 INSERM / UMR8199 CNRS, Institut Pasteur de Lille, Lille University Hospital, European Genomic Institute for Diabetes, University of Lille, Lille, France
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Sarah Filippi
- Department of Mathematics, Imperial College London, London, UK
| | - Michael J Cox
- University of Birmingham College of Medical and Dental Sciences, 150183, Institute of Microbiology and Infection, Birmingham, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sofia K Forslund
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK.
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