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Connell JT, Bouras G, Yeo K, Fenix K, Cooksley C, Bassiouni A, Vreugde S, Wormald PJ, Psaltis AJ. Characterising the allergic fungal rhinosinusitis microenvironment using full-length 16S rRNA gene amplicon sequencing and fungal ITS sequencing. Allergy 2024. [PMID: 39044721 DOI: 10.1111/all.16240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 07/25/2024]
Abstract
INTRODUCTION Allergic fungal rhinosinusitis (AFRS) is a severe phenotype of chronic rhinosinusitis with nasal polyposis (CRSwNP), characterised by localised and exaggerated type 2 inflammation. While fungal antigenic stimulation of unregulated Th2-mediated inflammation is the core pathophysiological mechanism, the direct and synergistic role of bacteria in disease modification is a pervasive hypothesis. We set out to define the microenvironment of AFRS to elucidate virulent organisms that may be implicated in the pathophysiology of AFRS. METHODOLOGY We undertook a cross-sectional study of AFRS patients and non-fungal CRSwNP patients. Demographics, disease severity, culture and microbiome sequences were analysed. Multimodality microbiome sequencing included short-read next-generation sequencing (NGS) on the Illumina Miseq (16S rRNA and ITS) and full-length 16S rRNA sequencing on the Oxford Nanopore Technologies GridION (ONT). RESULTS Thirty-two AFRS and 29 non-fungal CRSwNP patients (NF) were included in this study. Staphylococcus aureus was the dominant organism cultured and sequenced in both AFRS and NF groups (AFRS 27.54%; NF 18.04%; p = .07). Streptococcus pneumoniae (AFRS 12.31%; NF 0.98%; p = .03) and Haemophilus influenzae (AFRS 15.03%; NF 0.24%; p = .005) were significantly more abundant in AFRS. Bacterial diversity (Shannon's index) was considerably lower in AFRS relative to NF (AFRS 0.6; NF 1.0, p = .008). Aspergillus was the most cultured fungus in AFRS (10/32, 31.3%). The AFRS sequenced mycobiome was predominantly represented by Malassezia (43.6%), Curvularia (18.5%) and Aspergillus (16.8%), while the NF mycobiome was nearly exclusively Malassezia (84.2%) with an absence of Aspergillus or dematiaceous fungi. CONCLUSION A low diversity, dysbiotic microenvironment dominated by Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae characterised the bacterial microbiome of AFRS, with a mycobiome abundant in Malassezia, Aspergillus and Curvularia. While Staphylococcus aureus has been previously implicated in AFRS through enterotoxin superantigen potential, Streptococcus pneumoniae and Haemophilus influenzae are novel findings that may represent alternate cross-kingdom pathophysiological mechanisms.
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Affiliation(s)
- J T Connell
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
- Department of Otolaryngology, Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - G Bouras
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - K Yeo
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - K Fenix
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - C Cooksley
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - A Bassiouni
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
- Department of Otolaryngology, Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - S Vreugde
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - P J Wormald
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
- Department of Otolaryngology, Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - A J Psaltis
- Department of Surgery-Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
- Department of Otolaryngology, Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
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Philip M, Rudi K, Ormaasen I, Angell IL, Pettersen R, Keeley NB, Snipen LG. METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data. BMC Bioinformatics 2024; 25:237. [PMID: 38997633 PMCID: PMC11245806 DOI: 10.1186/s12859-024-05837-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 06/10/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing. RESULTS We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results. CONCLUSION Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment.
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Affiliation(s)
- Melcy Philip
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ida Ormaasen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Lars-Gustav Snipen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Sapoval N, Liu Y, Curry KD, Kille B, Huang W, Kokroko N, Nute MG, Tyshaieva A, Dilthey A, Molloy EK, Treangen TJ. Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596961. [PMID: 38895276 PMCID: PMC11185576 DOI: 10.1101/2024.06.01.596961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Taxonomic profiling is a ubiquitous task in the analysis of clinical and environmental microbiomes. The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling from long-read shotgun metagenomic datasets. Lemur is a marker-gene based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet makes detailed presence/absence calls for bacterial genomes based on whole-genome read mapping. The tools work in sequence: Lemur estimates abundances conservatively, and Magnet operates on the genomes of identified organisms to filter out likely false positive taxa. The result is an increase in precision of as much as 70%, which far exceeds competing methods. By operating only on marker genes, Lemur is a comparatively lightweight software. We demonstrate that it can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs - a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. The reference is available at https://zenodo.org/records/10802546, and the software is open-source and available at https://github.com/treangenlab/lemur.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Kristen D. Curry
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Bryce Kille
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Wenyu Huang
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Natalie Kokroko
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Michael G. Nute
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Alona Tyshaieva
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Dusseldorf, Düsseldorf, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Dusseldorf, Düsseldorf, Germany
| | - Erin K. Molloy
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX 77005, USA
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4
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Ota Y, Yasunaga K, Mahazu S, Prah I, Nagai S, Hayashi T, Suzuki M, Yoshida M, Hoshino Y, Akeda Y, Suzuki T, Gu Y, Saito R. Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities. J Microbiol Methods 2024; 221:106929. [PMID: 38599390 DOI: 10.1016/j.mimet.2024.106929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei Yasunaga
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan; Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Nagai
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Kanagawa, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiaki Gu
- Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan.
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Walsh CJ, Srinivas M, Stinear TP, van Sinderen D, Cotter PD, Kenny JG. GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences. Microb Genom 2024; 10:001255. [PMID: 38847800 PMCID: PMC11261877 DOI: 10.1099/mgen.0.001255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/07/2024] [Indexed: 07/24/2024] Open
Abstract
Sequence comparison of 16S rRNA PCR amplicons is an established approach to taxonomically identify bacterial isolates and profile complex microbial communities. One potential application of recent advances in long-read sequencing technologies is to sequence entire rRNA operons and capture significantly more phylogenetic information compared to sequencing of the 16S rRNA (or regions thereof) alone, with the potential to increase the proportion of amplicons that can be reliably classified to lower taxonomic ranks. Here we describe GROND (Genome-derived Ribosomal Operon Database), a publicly available database of quality-checked 16S-ITS-23S rRNA operons, accompanied by multiple taxonomic classifications. GROND will aid researchers in analysis of their data and act as a standardised database to allow comparison of results between studies.
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Affiliation(s)
- Calum J. Walsh
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Meghana Srinivas
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Timothy P. Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Douwe van Sinderen
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc Moorepark, Cork, Ireland
| | - John G. Kenny
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc Moorepark, Cork, Ireland
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6
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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; 21:954-966. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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7
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Shepherd AI, James TJ, Gould AAM, Mayes H, Neal R, Shute J, Tipton MJ, Massey H, Saynor ZL, Perissiou M, Montgomery H, Sturgess C, Makaronidis J, Murray AJ, Grocott MPW, Cummings M, Young-Min S, Rennell-Smyth J, McNarry MA, Mackintosh KA, Dent H, Robson SC, Corbett J. Impact of nocturnal hypoxia on glycaemic control, appetite, gut microbiota and inflammation in adults with type 2 diabetes mellitus: A single-blind cross-over trial. J Physiol 2024. [PMID: 38769692 DOI: 10.1113/jp285322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
High altitude residents have a lower incidence of type 2 diabetes mellitus (T2DM). Therefore, we examined the effect of repeated overnight normobaric hypoxic exposure on glycaemic control, appetite, gut microbiota and inflammation in adults with T2DM. Thirteen adults with T2DM [glycated haemoglobin (HbA1c): 61.1 ± 14.1 mmol mol-1; aged 64.2 ± 9.4 years; four female] completed a single-blind, randomised, sham-controlled, cross-over study for 10 nights, sleeping when exposed to hypoxia (fractional inspired O2 [F I O 2 ${{F}_{{\mathrm{I}}{{{\mathrm{O}}}_{\mathrm{2}}}}}$ ] = 0.155; ∼2500 m simulated altitude) or normoxic conditions (F I O 2 ${{F}_{{\mathrm{I}}{{{\mathrm{O}}}_{\mathrm{2}}}}}$ = 0.209) in a randomised order. Outcome measures included: fasted plasma [glucose]; [hypoxia inducible factor-1α]; [interleukin-6]; [tumour necrosis factor-α]; [interleukin-10]; [heat shock protein 70]; [butyric acid]; peak plasma [glucose] and insulin sensitivity following a 2 h oral glucose tolerance test; body composition; appetite indices ([leptin], [acyl ghrelin], [peptide YY], [glucagon-like peptide-1]); and gut microbiota diversity and abundance [16S rRNA amplicon sequencing]. During intervention periods, accelerometers measured physical activity, sleep duration and efficiency, whereas continuous glucose monitors were used to assess estimated HbA1c and glucose management indicator and time in target range. Overnight hypoxia was not associated with changes in any outcome measure (P > 0.05 with small effect sizes) except fasting insulin sensitivity and gut microbiota alpha diversity, which exhibited trends (P = 0.10; P = 0.08 respectively) for a medium beneficial effect (d = 0.49; d = 0.59 respectively). Ten nights of overnight moderate hypoxic exposure did not significantly affect glycaemic control, gut microbiome, appetite, or inflammation in adults with T2DM. However, the intervention was well tolerated and a medium effect-size for improved insulin sensitivity and reduced alpha diversity warrants further investigation. KEY POINTS: Living at altitude lowers the incidence of type 2 diabetes mellitus (T2DM). Animal studies suggest that exposure to hypoxia may lead to weight loss and suppressed appetite. In a single-blind, randomised sham-controlled, cross-over trial, we assessed the effects of 10 nights of hypoxia (fractional inspired O2 ∼0.155) on glucose homeostasis, appetite, gut microbiota, inflammatory stress ([interleukin-6]; [tumour necrosis factor-α]; [interleukin-10]) and hypoxic stress ([hypoxia inducible factor 1α]; heat shock protein 70]) in 13 adults with T2DM. Appetite and inflammatory markers were unchanged following hypoxic exposure, but an increased insulin sensitivity and reduced gut microbiota alpha diversity were associated with a medium effect-size and statistical trends, which warrant further investigation using a definitive large randomised controlled trial. Hypoxic exposure may represent a viable therapeutic intervention in people with T2DM and particularly those unable or unwilling to exercise because barriers to uptake and adherence may be lower than for other lifestyle interventions (e.g. diet and exercise).
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Affiliation(s)
- Anthony I Shepherd
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
- Clinical Health and Rehabilitation Team, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
- Diabetes and Endocrinology Department, Portsmouth Hospitals University NHS Trust, Portsmouth, UK
| | - Thomas J James
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
- Clinical Health and Rehabilitation Team, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Alex A M Gould
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Harry Mayes
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Rebecca Neal
- Department of Rehabilitation and Sport Sciences, Bournemouth University, Poole, UK
| | - Janis Shute
- School of Pharmacy and Biomedical Sciences, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Michael J Tipton
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Heather Massey
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Zoe L Saynor
- Clinical Health and Rehabilitation Team, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Maria Perissiou
- Clinical Health and Rehabilitation Team, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Hugh Montgomery
- Centre for Human Health and Performance, Dept Medicine, University College London, London, UK
| | - Connie Sturgess
- Centre for Human Health and Performance, Dept Medicine, University College London, London, UK
| | - Janine Makaronidis
- Centre for Obesity Research, University College London, London, UK
- National Institute for Health and Care Research, University College London Hospitals Biomedical Research Centre, London, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Michael P W Grocott
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton & University of Southampton, Southampton, UK
| | - Michael Cummings
- Diabetes and Endocrinology Department, Portsmouth Hospitals University NHS Trust, Portsmouth, UK
| | - Steven Young-Min
- Rheumatology Department, Portsmouth Hospitals University NHS Trust, Portsmouth, UK
| | - Janet Rennell-Smyth
- Clinical Health and Rehabilitation Team, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
- Patient and public involvement member
| | - Melitta A McNarry
- School of Biological Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Kelly A Mackintosh
- School of Biological Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Hannah Dent
- School of Pharmacy and Biomedical Sciences, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
- Institute of Life Sciences and Healthcare, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Samuel C Robson
- School of Pharmacy and Biomedical Sciences, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
- Applied Sports, Technology, Exercise and Medicine (A-STEM) Research Centre, School of Sport and Exercise Sciences, Swansea University, Swansea, UK
- Institute of Life Sciences and Healthcare, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - Jo Corbett
- Extreme Environments Laboratory, School of Sport, Health and Exercise Science, Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
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Erlandson SR, Ewing PM, Osborne SL, Lehman RM. Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations. ENVIRONMENTAL MICROBIOME 2024; 19:30. [PMID: 38715076 PMCID: PMC11077770 DOI: 10.1186/s40793-024-00571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/21/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method. RESULTS Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations. CONCLUSIONS Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.
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Affiliation(s)
- Sonya R Erlandson
- USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA.
| | - Patrick M Ewing
- USDA-ARS-Food Systems Research Unit, Burlington, VT, 57006, USA
| | - Shannon L Osborne
- USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA
| | - R Michael Lehman
- USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA
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9
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Yeo K, Connell J, Bouras G, Smith E, Murphy W, Hodge JC, Krishnan S, Wormald PJ, Valentine R, Psaltis AJ, Vreugde S, Fenix KA. A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues. Arch Microbiol 2024; 206:248. [PMID: 38713383 PMCID: PMC11076400 DOI: 10.1007/s00203-024-03985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/28/2024] [Indexed: 05/08/2024]
Abstract
Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina) in 26 HNC tumour tissues. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. We observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.131, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in relative abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (75% vs. 18.8%). FL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing.
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Affiliation(s)
- Kenny Yeo
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia.
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.
| | - James Connell
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - George Bouras
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Eric Smith
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - William Murphy
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - John-Charles Hodge
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Otolaryngology, Head and Neck Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Suren Krishnan
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Otolaryngology, Head and Neck Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Peter-John Wormald
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Rowan Valentine
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Alkis James Psaltis
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Sarah Vreugde
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Kevin Aaron Fenix
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia.
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.
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10
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Lou EG, Fu Y, Wang Q, Treangen TJ, Stadler LB. Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133939. [PMID: 38490149 DOI: 10.1016/j.jhazmat.2024.133939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
Wastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge is selecting which analytical tool to deploy to measure risk indicators, such as antibiotic resistance genes (ARGs) and their respective bacterial hosts. Although metagenomics is frequently used for analyzing ARGs, few studies have compared the performance of long-read and short-read metagenomics in identifying which bacteria harbor ARGs in wastewater. Furthermore, for ARG host detection, untargeted metagenomics has not been compared to targeted methods such as epicPCR. Here, we 1) evaluated long-read and short-read metagenomics as well as epicPCR for detecting ARG hosts in wastewater, and 2) investigated the host range of ARGs across the wastewater treatment plant (WWTP) to evaluate host proliferation. Results highlighted long-read revealed a wider range of ARG hosts compared to short-read metagenomics. Nonetheless, the ARG host range detected by long-read metagenomics only represented a subset of the hosts detected by epicPCR. The ARG-host linkages across the influent and effluent of the WWTP were characterized. Results showed the ARG-host phylum linkages were relatively consistent across the WWTP, whereas new ARG-host species linkages appeared in the WWTP effluent. The ARG-host linkages of several clinically relevant species found in the effluent were identified.
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Affiliation(s)
- Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Qi Wang
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.
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11
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Dixon MM, Afkairin A, Davis JG, Chitwood-Brown J, Buchanan CM, Ippolito JA, Manter DK, Vivanco JM. Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery. Sci Rep 2024; 14:9934. [PMID: 38689014 PMCID: PMC11061195 DOI: 10.1038/s41598-024-60775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
Legacy phosphorus (P) is a reservoir of sparingly available P, and its recovery could enhance sustainable use of nonrenewable mineral fertilizers. Domestication has affected P acquisition, but it is unknown if subsequent breeding efforts, like the Green Revolution (GR), had a similar effect. We examined how domestication and breeding events altered P acquisition by growing wild, traditional (pre-GR), and modern (post-GR) tomato in soil with legacy P but low bioavailable P. Wild tomatoes, particularly accession LA0716 (Solanum pennellii), heavily cultured rhizosphere P solubilizers, suggesting reliance on microbial associations to acquire P. Wild tomato also had a greater abundance of other putatively beneficial bacteria, including those that produce chelating agents and antibiotic compounds. Although wild tomatoes had a high abundance of these P solubilizers, they had lower relative biomass and greater P stress factor than traditional or modern tomato. Compared to wild tomato, domesticated tomato was more tolerant to P deficiency, and both cultivated groups had a similar rhizosphere bacterial community composition. Ultimately, this study suggests that while domestication changed tomato P recovery by reducing microbial associations, subsequent breeding processes have not further impacted microbial P acquisition mechanisms. Selecting microbial P-related traits that diminished with domestication may therefore increase legacy P solubilization.
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Affiliation(s)
- Mary M Dixon
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Antisar Afkairin
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Jessica G Davis
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jessica Chitwood-Brown
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Cassidy M Buchanan
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - James A Ippolito
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- United States Department of Agriculture-Agricultural Research Service, Soil Management and Sugar Beet Research, Fort Collins, CO, USA
| | - Daniel K Manter
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA.
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12
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Konovalovas A, Armalytė J, Klimkaitė L, Liveikis T, Jonaitytė B, Danila E, Bironaitė D, Mieliauskaitė D, Bagdonas E, Aldonytė R. Human nasal microbiota shifts in healthy and chronic respiratory disease conditions. BMC Microbiol 2024; 24:150. [PMID: 38678223 PMCID: PMC11055347 DOI: 10.1186/s12866-024-03294-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND An increasing number of studies investigate various human microbiotas and their roles in the development of diseases, maintenance of health states, and balanced signaling towards the brain. Current data demonstrate that the nasal microbiota contains a unique and highly variable array of commensal bacteria and opportunistic pathogens. However, we need to understand how to harness current knowledge, enrich nasal microbiota with beneficial microorganisms, and prevent pathogenic developments. RESULTS In this study, we have obtained nasal, nasopharyngeal, and bronchoalveolar lavage fluid samples from healthy volunteers and patients suffering from chronic respiratory tract diseases for full-length 16 S rRNA sequencing analysis using Oxford Nanopore Technologies. Demographic and clinical data were collected simultaneously. The microbiome analysis of 97 people from Lithuania suffering from chronic inflammatory respiratory tract disease and healthy volunteers revealed that the human nasal microbiome represents the microbiome of the upper airways well. CONCLUSIONS The nasal microbiota of patients was enriched with opportunistic pathogens, which could be used as indicators of respiratory tract conditions. In addition, we observed that a healthy human nasal microbiome contained several plant- and bee-associated species, suggesting the possibility of enriching human nasal microbiota via such exposures when needed. These candidate probiotics should be investigated for their modulating effects on airway and lung epithelia, immunogenic properties, neurotransmitter content, and roles in maintaining respiratory health and nose-brain interrelationships.
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Affiliation(s)
- Aleksandras Konovalovas
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Julija Armalytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania.
| | - Laurita Klimkaitė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Tomas Liveikis
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Brigita Jonaitytė
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Edvardas Danila
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Centre of Pulmonology and Allergology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Daiva Bironaitė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | | | - Edvardas Bagdonas
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Rūta Aldonytė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania.
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13
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Veselovsky VA, Boldyreva DI, Olekhnovich EI, Klimina KM, Babenko VV, Zakharevich NV, Larin AK, Morozov MD, Zoruk PY, Sergiev PV, Dontsova OA, Maev IV, Novik TS, Kotlobay AA, Lazarev VN, Lagarkova MA. Effect of the consumption of brazzein and monellin, two recombinant sweet-tasting proteins, on rat gut microbiota. Front Nutr 2024; 11:1362529. [PMID: 38577158 PMCID: PMC10991754 DOI: 10.3389/fnut.2024.1362529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Sweet-tasting proteins (SPs) are proteins of plant origin initially isolated from tropical fruits. They are thousands of times sweeter than sucrose and most artificial sweeteners. SPs are a class of proteins capable of causing a sweet taste sensation in humans when interacting with the T1R2/T1R3 receptor. SP thaumatin has already been introduced in the food industry in some countries. Other SPs, such as monellin and brazzein, are promising products. An important stage in researching SPs, in addition to confirming the absence of toxicity, mutagenicity, oncogenicity, and allergenic effects, is studying their influence on gut microbiota. In this paper we describe changes in the composition of rat gut microbiota after six months of consuming one of two recombinant SPs-brazzein or monellin. A full length 16S gene sequencing method was used for DNA library barcoding. The MaAsLin2 analysis results showed noticeable fluctuations in the relative abundances of Anaerocella delicata in brazzein-fed rat microbiota, and of Anaerutruncus rubiinfantis in monellin-fed rat microbiota, which, however, did not exceed the standard deviation. The sucrose-fed group was associated with an increase in the relative abundance of Faecalibaculum rodentium, which may contribute to obesity. Overall, prolonged consumption of the sweet proteins brazzein and monellin did not significantly change rat microbiota and did not result in the appearance of opportunistic microbiota. This provides additional evidence for the safety of these potential sweeteners.
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Affiliation(s)
- Vladimir A. Veselovsky
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Daria I. Boldyreva
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Evgenii I. Olekhnovich
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Ksenia M. Klimina
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Vladislav V. Babenko
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Natalia V. Zakharevich
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Andrey K. Larin
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Maxim D. Morozov
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Polina Y. Zoruk
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Petr V. Sergiev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Igor V. Maev
- Department of Propaedeutics of Internal Diseases and Gastroenterology, Moscow State University of Medicine and Dentistry, Moscow, Russia
| | | | - Anatoly A. Kotlobay
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Vassili N. Lazarev
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Maria A. Lagarkova
- Lopukhin Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
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14
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Zhang S, Deng Z, Yin X, Fang H, Song G, Liu Y, Jiang X, Wang X, Wang L. Bioaccessibility of lead and cadmium in soils around typical lead-acid power plants and their effect on gut microorganisms. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:107. [PMID: 38446285 DOI: 10.1007/s10653-023-01840-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/18/2023] [Indexed: 03/07/2024]
Abstract
Potentially toxic elements (Pb and Cd) contamination of soil can adversely affect human health. Moreover, these metal ions interact with the gut microbiota after entering the human digestive system. Based on the physiologically based extraction test and the simulator of human intestinal microbial ecosystem, the bioaccessibility of Pb and Cd in soils contaminated with lead-acid power plants was assessed. The gastric stage exhibited the greatest average bioaccessibility of lead and cadmium (63.39% and 57.22%), followed by the small intestinal stage (6.86% and 36.29%); due to gut microorganisms, the bioaccessibility of lead and cadmium was further reduced in the colon stage (1.86% and 4.22%). Furthermore, to investigate soil contamination's effects on gut microbes, 16S rRNA high-throughput sequencing was used to identify the gut microbial species after the colon period. Due to Pb and Cd exposure, the relative abundance of Firmicutes and unidentified_Bacteria decreased, while the relative abundance of Proteobacteria, Synergistota, and Bacteroidota increased. The relationship between environmental factors and the number of microbial species in the gut was also examined using Spearman correlation analysis. Pb and Cd exposure has been found to affect the composition and structure of the gut microbiota.
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Affiliation(s)
- Shuxi Zhang
- Shandong Analysis and Test Center,, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Zhiwen Deng
- Shandong Analysis and Test Center,, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xixiang Yin
- Shandong Jinan Eco-Environmental Monitoring Center, Jinan, 250101, China.
| | - Hongke Fang
- Shandong Jinan Eco-Environmental Monitoring Center, Jinan, 250101, China
| | - Guangmin Song
- Shandong Jinan Eco-Environmental Monitoring Center, Jinan, 250101, China
| | - Yuanyuan Liu
- Shandong Analysis and Test Center,, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xiyan Jiang
- Shandong Analysis and Test Center,, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xiaodong Wang
- School of Civil Engineering and Architecture, University of Jinan, Jinan, 250022, China
| | - Lihong Wang
- Shandong Analysis and Test Center,, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China.
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15
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Li L, He XZ, Wang M, Huang L, Wang Z, Zhang X, Hu J, Hou F. Grazing-driven shifts in soil bacterial community structure and function in a typical steppe are mediated by additional N inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169488. [PMID: 38142006 DOI: 10.1016/j.scitotenv.2023.169488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/16/2023] [Accepted: 12/17/2023] [Indexed: 12/25/2023]
Abstract
Herbivore grazing and nitrogen (N) fertilization affect soil microbial diversity and community composition both in direct and indirect pathways (e.g., via alterations in soil microenvironment and plant communities); however, their combination effects are still largely unexplored. We carried out a field study to investigate how soil abiotic properties, plant community composition and functional traits altered soil bacterial community structure and function in response to a long-term herbivore grazing (17-year sheep grazing with four stocking rates) and anthropogenic N inputs (6-year N addition with four levels) experiment. We show that a high stocking rate of 8.7 sheep ha-1 (SR8.7) decreased soil bacterial α- and β-diversity, while α- and β-diversity showed hump-shaped and saddle-shaped responses, respectively, with increasing N addition rate, reaching tipping points at the N application rate of 10 g N m-2 year-1 (N10). The synergistic effects of grazing and N addition induced the highest soil bacterial α-diversity at SR2.7 with N10. The contrasting effects of grazing and N addition induced higher soil bacterial β-diversity at SR8.7 with N20. Plant factors (e.g., aboveground biomass of Stipa bungeana and community-weighted mean carbon [CWM_C]), edaphic factors (e.g., soil moisture, pH, NO3--N, and C:nutrients ratios) and their interactions were the most significant factors affecting the diversity and community composition of bacteria. Our structure equation model (SEM) shows that grazing-induced negative effects on soil pH and plant community composition indirectly increased the β-diversity of soil bacteria, while grazing-induced decreased CWM_C had positive effects on bacterial α-diversity and community structure. However, N addition indirectly increased β-diversity of soil bacteria via changes in soil NO3--N and plant community composition, while N addition had negative impacts on bacterial α-diversity and community structure via variations in CWM_C. The interaction of grazing and N addition increased the complexity and stability of the bacterial network. Based on the KEGG database, grazing and N addition could accelerate the soil functional potential of C and N cycling. Our findings suggest that N application at a rate of <10 g N m-2 year-1 with a stocking rate of <5.3 sheep ha-1 could maintain the development of soil bacteria in supporting the most important ecosystem functions and services. Complex responses of soil microbes to grazing and N addition indicate the need for deeper investigations of the impacts of global change on microbial involvement in biogeochemical cycles.
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Affiliation(s)
- Lan Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiong Zhao He
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Mengyuan Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ling Huang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Zhen Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiumin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Junqi Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Technology Research Center for Ecological Restoration and Utilization of Degraded Grassland in Northwest China, National Forestry and Grassland Administration; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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16
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Kuruwa S, Zade A, Shah S, Moidu R, Lad S, Chande C, Joshi A, Hirani N, Nikam C, Bhattacharya S, Poojary A, Kapoor M, Kondabagil K, Chatterjee A. An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG. J Appl Microbiol 2024; 135:lxae037. [PMID: 38346849 DOI: 10.1093/jambio/lxae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
AIMS The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs). METHODS AND RESULTS The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible. CONCLUSION NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.
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Affiliation(s)
- Sanjana Kuruwa
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rameez Moidu
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh Lad
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chhaya Chande
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Ameeta Joshi
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Nilma Hirani
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Chaitali Nikam
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Thyrocare Technologies Pvt. Ltd, Navi Mumbai 400703, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, 14, MAR(E-W), DH Block (Newtown), Action Area I, Newtown, Kolkata, Chakpachuria 700160, India
| | - Aruna Poojary
- Department of Microbiology, Breach Candy Hospital and Research Center, Mumbai 400026, India
| | - Mahua Kapoor
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anirvan Chatterjee
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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17
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Yeo K, Li R, Wu F, Bouras G, Mai LTH, Smith E, Wormald PJ, Valentine R, Psaltis AJ, Vreugde S, Fenix K. Identification of consensus head and neck cancer-associated microbiota signatures: a systematic review and meta-analysis of 16S rRNA and The Cancer Microbiome Atlas datasets. J Med Microbiol 2024; 73. [PMID: 38299619 DOI: 10.1099/jmm.0.001799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Introduction. Multiple reports have attempted to describe the tumour microbiota in head and neck cancer (HNSC).Gap statement. However, these have failed to produce a consistent microbiota signature, which may undermine understanding the importance of bacterial-mediated effects in HNSC.Aim. The aim of this study is to consolidate these datasets and identify a consensus microbiota signature in HNSC.Methodology. We analysed 12 published HNSC 16S rRNA microbial datasets collected from cancer, cancer-adjacent and non-cancer tissues to generate a consensus microbiota signature. These signatures were then validated using The Cancer Microbiome Atlas (TCMA) database and correlated with the tumour microenvironment phenotypes and patient's clinical outcome.Results. We identified a consensus microbial signature at the genus level to differentiate between HNSC sample types, with cancer and cancer-adjacent tissues sharing more similarity than non-cancer tissues. Univariate analysis on 16S rRNA datasets identified significant differences in the abundance of 34 bacterial genera among the tissue types. Paired cancer and cancer-adjacent tissue analyses in 16S rRNA and TCMA datasets identified increased abundance in Fusobacterium in cancer tissues and decreased abundance of Atopobium, Rothia and Actinomyces in cancer-adjacent tissues. Furthermore, these bacteria were associated with different tumour microenvironment phenotypes. Notably, high Fusobacterium signature was associated with high neutrophil (r=0.37, P<0.0001), angiogenesis (r=0.38, P<0.0001) and granulocyte signatures (r=0.38, P<0.0001) and better overall patient survival [continuous: HR 0.8482, 95 % confidence interval (CI) 0.7758-0.9273, P=0.0003].Conclusion. Our meta-analysis demonstrates a consensus microbiota signature for HNSC, highlighting its potential importance in this disease.
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Affiliation(s)
- Kenny Yeo
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Runhao Li
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Fangmeinuo Wu
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - George Bouras
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Linh T H Mai
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Eric Smith
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Peter-John Wormald
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Rowan Valentine
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Alkis James Psaltis
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Sarah Vreugde
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
| | - Kevin Fenix
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide SA, 5000, Australia
- Department of Surgery- Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South SA, 5011, Australia
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18
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Zhao B, Liu R, Li Y, Xu H, Li X, Gu J, Zhang X, Wang Y, Wang Y. Changes of putative pathogenic species within the water bacterial community in large-scale drinking water treatment and distribution systems. WATER RESEARCH 2024; 249:120947. [PMID: 38043356 DOI: 10.1016/j.watres.2023.120947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Although the management of microbes in drinking water is of paramount importance for public health, there remain challenges in comprehensively examining pathogenic bacteria in the water supply system at the species level. In this study, high-throughput sequencing of nearly full-length 16S rRNA genes was performed to investigate the changes of the water bacterial community in three large-scale drinking water treatment plants (DWTPs) and their corresponding distribution systems during winter and summer. Our findings revealed significant differences in the bacterial community structure between winter and summer water samples for each DWTP and its distribution management area (DMA). In the groundwater-fed DWTP, selective enrichment of mycobacterial species was observed in both seasons, and the subsequent DMA also exhibited strong selection for specific mycobacterial species. In one of the surface water-fed DWTPs, certain Legionella species present in the source water in winter were selectively enriched in the bacterial community after pre-oxidation, although they were susceptible to the subsequent purification steps. A variety of putative pathogenic species (n = 83) were identified based on our pathogen identification pipeline, with the dominant species representing opportunistic pathogens commonly found in water supply systems. While pathogen removal primarily occurred during the purification processes of DWTPs, especially for surface water-fed plants, the relative abundance of pathogenic bacteria in the DMA water flora was lower than that in the DWTP effluent flora, indicating a diminished competitiveness of pathogens within the DMA ecosystem.
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Affiliation(s)
- Bei Zhao
- Beijing Waterworks Group Co., Ltd, Beijing, PR China; Beijing Engineering Research Center for Drinking Water Quality, Beijing, PR China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China; Weiqiao-UCAS Science and Technology Park, Binzhou Institute of Technology, Binzhou, Shandong, PR China.
| | - Yuxian Li
- Beijing Waterworks Group Co., Ltd, Beijing, PR China; Beijing Engineering Research Center for Drinking Water Quality, Beijing, PR China
| | - Hao Xu
- Beijing Waterworks Group Co., Ltd, Beijing, PR China; Beijing Engineering Research Center for Drinking Water Quality, Beijing, PR China
| | - Xiangyi Li
- Beijing Waterworks Group Co., Ltd, Beijing, PR China; Beijing Engineering Research Center for Drinking Water Quality, Beijing, PR China
| | - Junnong Gu
- Beijing Waterworks Group Co., Ltd, Beijing, PR China; Beijing Engineering Research Center for Drinking Water Quality, Beijing, PR China
| | - Xiaolan Zhang
- Beijing Waterworks Group Co., Ltd, Beijing, PR China; Beijing Engineering Research Center for Drinking Water Quality, Beijing, PR China
| | - Yue Wang
- Beijing Waterworks Group Co., Ltd, Beijing, PR China
| | - Yansong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
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19
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Wu Q, Badu S, So SY, Treangen TJ, Savidge TC. The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease. J Clin Invest 2024; 134:e170859. [PMID: 37962956 PMCID: PMC10786686 DOI: 10.1172/jci170859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Targeted metagenomic sequencing is an emerging strategy to survey disease-specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results owing to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via reanalysis of individual patient 16S data sets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome, or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new "best practices" approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level.
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Affiliation(s)
- Qinglong Wu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Shyam Badu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Sik Yu So
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Tor C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
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20
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Lao HY, Wong LLY, Hui Y, Ng TTL, Chan CTM, Lo HWH, Yau MCY, Leung ECM, Wong RCW, Ho AYM, Yip KT, Lam JYW, Chow VCY, Luk KS, Que TL, Chow FWN, Siu GKH. The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids. Front Microbiol 2024; 14:1324494. [PMID: 38264489 PMCID: PMC10803466 DOI: 10.3389/fmicb.2023.1324494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.
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Affiliation(s)
- Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lily Lok-Yee Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Yan Hui
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hazel Wing-Hei Lo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Miranda Chong-Yee Yau
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Eddie Chi-Man Leung
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - River Chun-Wai Wong
- Department of Microbiology, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Kowloon, Hong Kong SAR, China
| | - Kam-Tong Yip
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong SAR, China
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Viola Chi-Ying Chow
- Department of Microbiology, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Kowloon, Hong Kong SAR, China
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong SAR, China
| | - Franklin Wang Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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21
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Sapoval N, Tanevski M, Treangen TJ. KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024; 29:506-520. [PMID: 38160303 PMCID: PMC10764071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The microbes present in the human gastrointestinal tract are regularly linked to human health and disease outcomes. Thanks to technological and methodological advances in recent years, metagenomic sequencing data, and computational methods designed to analyze metagenomic data, have contributed to improved understanding of the link between the human gut microbiome and disease. However, while numerous methods have been recently developed to extract quantitative and qualitative results from host-associated microbiome data, improved computational tools are still needed to track microbiome dynamics with short-read sequencing data. Previously we have proposed KOMB as a de novo tool for identifying copy number variations in metagenomes for characterizing microbial genome dynamics in response to perturbations. In this work, we present KombOver (KO), which includes four key contributions with respect to our previous work: (i) it scales to large microbiome study cohorts, (ii) it includes both k-core and K-truss based analysis, (iii) we provide the foundation of a theoretical understanding of the relation between various graph-based metagenome representations, and (iv) we provide an improved user experience with easier-to-run code and more descriptive outputs/results. To highlight the aforementioned benefits, we applied KO to nearly 1000 human microbiome samples, requiring less than 10 minutes and 10 GB RAM per sample to process these data. Furthermore, we highlight how graph-based approaches such as k-core and K-truss can be informative for pinpointing microbial community dynamics within a myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) cohort. KO is open source and available for download/use at: https://github.com/treangenlab/komb.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX 77005, USA,
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22
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Berkovich AK, Pyshkina OA, Zorina AA, Rodin VA, Panova TV, Sergeev VG, Zvereva ME. Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S234-S248. [PMID: 38621753 DOI: 10.1134/s000629792414013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 04/17/2024]
Abstract
This review highlights operational principles, features, and modern aspects of the development of third-generation sequencing technology of biopolymers focusing on the nucleic acids analysis, namely the nanopore sequencing system. Basics of the method and technical solutions used for its realization are considered, from the first works showing the possibility of creation of these systems to the easy-to-handle procedure developed by Oxford Nanopore Technologies company. Moreover, this review focuses on applications, which were developed and realized using equipment developed by the Oxford Nanopore Technologies, including assembly of whole genomes, methagenomics, direct analysis of the presence of modified bases.
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Affiliation(s)
- Anna K Berkovich
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Olga A Pyshkina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna A Zorina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir A Rodin
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatyana V Panova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir G Sergeev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria E Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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23
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Olivier SA, Bull MK, Strube ML, Murphy R, Ross T, Bowman JP, Chapman B. Long-read MinION™ sequencing of 16S and 16S-ITS-23S rRNA genes provides species-level resolution of Lactobacillaceae in mixed communities. Front Microbiol 2023; 14:1290756. [PMID: 38143859 PMCID: PMC10740194 DOI: 10.3389/fmicb.2023.1290756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
The Lactobacillaceae are lactic acid bacteria harnessed to deliver important outcomes across numerous industries, and their unambiguous, species-level identification from mixed community environments is an important endeavor. Amplicon-based metataxonomics using short-read sequencing of partial 16S rRNA gene regions is widely used to support this, however, the high genetic similarity among Lactobacillaceae species restricts our ability to confidently describe these communities even at genus level. Long-read sequencing (LRS) of the whole 16S rRNA gene or the near complete rRNA operon (16S-ITS-23S) has the potential to improve this. We explored species ambiguity amongst Lactobacillaceae using in-silico tool RibDif2, which identified allele overlap when various partial and complete 16S rRNA gene and 16S-ITS-23S rRNA regions were amplified. We subsequently implemented LRS by MinION™ to compare the capacity of V3-V4, 16S and 16S-ITS-23S rRNA amplicons to accurately describe the diversity of a 20-species Lactobacillaceae mock community in practice. In-silico analysis identified more instances of allele/species overlap with V3-V4 amplicons (n = 43) compared to the 16S rRNA gene (n = 11) and partial (n = up to 15) or complete (n = 0) 16S-ITS-23S rRNA amplicons. With subsequent LRS of a DNA mock community, 80% of target species were identified using V3-V4 amplicons whilst the 16S rRNA gene and 16S-ITS-23S rRNA region amplicons resulted in 95 and 100% of target species being identified. A considerable reduction in false-positive identifications was also seen with 16S rRNA gene (n = 3) and 16S-ITS-23S rRNA region (n = 9) amplicons compared with V3-V4 amplicons (n = 43). Whilst the target species affected by allele overlap in V3-V4 and 16S rRNA gene sequenced mock communities were predicted by RibDif2, unpredicted species ambiguity was observed in 16S-ITS-23S rRNA sequenced communities. Considering the average nucleotide identity (ANI) between ambiguous species (~97%) and the basecall accuracy of our MinION™ sequencing protocol (96.4%), the misassignment of reads between closely related taxa is to be expected. With basecall accuracy exceeding 99% for recent MinION™ releases, the increased species-level differentiating power promised by longer amplicons like the 16S-ITS-23S rRNA region, may soon be fully realized.
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Affiliation(s)
- Sandra A. Olivier
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- Quantal Bioscience Pty Ltd., Sydney, NSW, Australia
| | - Michelle K. Bull
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- Quantal Bioscience Pty Ltd., Sydney, NSW, Australia
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Robert Murphy
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Tom Ross
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Belinda Chapman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- Quantal Bioscience Pty Ltd., Sydney, NSW, Australia
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24
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Ghielmetti G, Loubser J, Kerr TJ, Stuber T, Thacker T, Martin LC, O'Hare MA, Mhlophe SK, Okunola A, Loxton AG, Warren RM, Moseley MH, Miller MA, Goosen WJ. Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing. Front Microbiol 2023; 14:1307440. [PMID: 38075895 PMCID: PMC10699144 DOI: 10.3389/fmicb.2023.1307440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.
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Affiliation(s)
- Giovanni Ghielmetti
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tanya J. Kerr
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Tyler Thacker
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Lauren C. Martin
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michaela A. O'Hare
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sinegugu K. Mhlophe
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Abisola Okunola
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark H. Moseley
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Michele A. Miller
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wynand J. Goosen
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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25
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Chen J, Xu F. Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections. Mol Diagn Ther 2023; 27:685-701. [PMID: 37563539 PMCID: PMC10590290 DOI: 10.1007/s40291-023-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
This review provides an in-depth discussion of the development, principles and utility of nanopore sequencing technology and its diverse applications in the identification of various pulmonary pathogens. We examined the emergence and advancements of nanopore sequencing as a significant player in this field. We illustrate the challenges faced in diagnosing mixed infections and further scrutinize the use of nanopore sequencing in the identification of single pathogens, including viruses (with a focus on its use in epidemiology, outbreak investigation, and viral resistance), bacteria (emphasizing 16S targeted sequencing, rare bacterial lung infections, and antimicrobial resistance studies), fungi (employing internal transcribed spacer sequencing), tuberculosis, and atypical pathogens. Furthermore, we discuss the role of nanopore sequencing in metagenomics and its potential for unbiased detection of all pathogens in a clinical setting, emphasizing its advantages in sequencing genome repeat areas and structural variant regions. We discuss the limitations in dealing with host DNA removal, the inherent high error rate of nanopore sequencing technology, along with the complexity of operation and processing, while acknowledging the possibilities provided by recent technological improvements. We compared nanopore sequencing with the BioFire system, a rapid molecular diagnostic system based on polymerase chain reaction. Although the BioFire system serves well for the rapid screening of known and common pathogens, it falls short in the identification of unknown or rare pathogens and in providing comprehensive genome analysis. As technological advancements continue, it is anticipated that the role of nanopore sequencing technology in diagnosing and treating lung infections will become increasingly significant.
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Affiliation(s)
- Jie Chen
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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Zhang T, Li H, Ma S, Cao J, Liao H, Huang Q, Chen W. The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling. Appl Environ Microbiol 2023; 89:e0060523. [PMID: 37800969 PMCID: PMC10617388 DOI: 10.1128/aem.00605-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/04/2023] [Indexed: 10/07/2023] Open
Abstract
The long-read amplicon provides a species-level solution for the community. With the improvement of nanopore flowcells, the accuracy of Oxford Nanopore Technologies (ONT) R10.4.1 has been substantially enhanced, with an average of approximately 99%. To evaluate its effectiveness on amplicons, three types of microbiomes were analyzed by 16S ribosomal RNA (hereinafter referred to as "16S") amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1) in the current study. We showed the error rate, recall, precision, and bias index in the mock sample. The error rate of ONT R10.4.1 was greatly reduced, with a better recall in the case of the synthetic community. Meanwhile, in different types of environmental samples, ONT R10.4.1 analysis resulted in a composition similar to Pacbio data. We found that classification tools and databases influence ONT data. Based on these results, we conclude that the ONT R10.4.1 16S amplicon can also be used for application in environmental samples. IMPORTANCE The long-read amplicon supplies the community with a species-level solution. Due to the high error rate of nanopore sequencing early on, it has not been frequently used in 16S studies. Oxford Nanopore Technologies (ONT) introduced the R10.4.1 flowcell with Q20+ reagent to achieve more than 99% accuracy as sequencing technology advanced. However, there has been no published study on the performance of commercial PromethION sequencers with R10.4.1 flowcells on 16S sequencing or on the impact of accuracy improvement on taxonomy (R9.4.1 to R10.4.1) using 16S ONT data. In this study, three types of microbiomes were investigated by 16S ribosomal RNA (rRNA) amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1). In the mock sample, we displayed the error rate, recall, precision, and bias index. We observed that the error rate in ONT R10.4.1 is significantly lower, especially when deletions are involved. First and foremost, R10.4.1 and Pacific Bioscience platforms reveal a similar microbiome in environmental samples. This study shows that the R10.4.1 full-length 16S rRNA sequences allow for species identification of environmental microbiota.
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Affiliation(s)
- Tianyuan Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Wuhan Benagen Technology Co., Ltd., Wuhan, China
| | - Hanzhou Li
- Wuhan Benagen Technology Co., Ltd., Wuhan, China
| | - Silin Ma
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jian Cao
- Wuhan Benagen Technology Co., Ltd., Wuhan, China
| | - Hao Liao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Kim J, Kim BS. Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster. J Microbiol Biotechnol 2023; 33:1162-1169. [PMID: 37415086 PMCID: PMC10580894 DOI: 10.4014/jmb.2302.02007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/06/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.
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Affiliation(s)
- Jaeeun Kim
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
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Mesloub Y, Beury D, Vandermeeren F, Caboche S. CuReSim-LoRM: A Tool to Simulate Metabarcoding Long Reads. Int J Mol Sci 2023; 24:14005. [PMID: 37762307 PMCID: PMC10531135 DOI: 10.3390/ijms241814005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Metabarcoding DNA sequencing has revolutionized the study of microbial communities. Third-generation sequencing producing long reads had opened up new perspectives. Obtaining the full-length ribosomal RNA gene would permit one to reach a better taxonomic resolution at the species or the strain level. However, Oxford Nanopore Technologies (ONT) sequencing produces reads with high error rates, which introduces biases in analysis. Understanding the biases introduced during the analysis allows one to better interpret the biological results and take care of conclusions drawn from metabarcoding experiments. To benchmark an analysis process, the ground truth, i.e., the real composition of the microbial community, has to be known. In addition to artificial mock communities, simulated data are often used to evaluate the biases and performances of the bioinformatics analysis step. Currently, no specific tool has been developed to simulate metabarcoding long reads, mimic the error rate and the length distribution, and allow one to benchmark the analysis process. Here, we introduce CuReSim-LoRM, for the customized read simulator to generate long reads for metabarcoding. We showed that CuReSim-LoRM is able to produce reads with varying error rates and length distributions by mimicking the real data very well.
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Affiliation(s)
| | | | | | - Ségolène Caboche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, F-59000 Lille, France
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Chen Q, Liu M, Guo H, Wang K, Liu J, Wang Y, Lin Y, Li J, Li P, Yang L, Jia L, Yang J, Li P, Song H. Altered Respiratory Microbiomes, Plasma Metabolites, and Immune Responses in Influenza A Virus and Methicillin-Resistant Staphylococcus aureus Coinfection. Microbiol Spectr 2023; 11:e0524722. [PMID: 37318361 PMCID: PMC10433956 DOI: 10.1128/spectrum.05247-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/29/2023] [Indexed: 06/16/2023] Open
Abstract
Influenza A virus (IAV)-methicillin-resistant Staphylococcus aureus (MRSA) coinfection causes severe respiratory infections. The host microbiome plays an important role in respiratory tract infections. However, the relationships among the immune responses, metabolic characteristics, and respiratory microbial characteristics of IAV-MRSA coinfection have not been fully studied. We used specific-pathogen-free (SPF) C57BL/6N mice infected with IAV and MRSA to build a nonlethal model of IAV-MRSA coinfection and characterized the upper respiratory tract (URT) and lower respiratory tract (LRT) microbiomes at 4 and 13 days postinfection by full-length 16S rRNA gene sequencing. Immune response and plasma metabolism profile analyses were performed at 4 days postinfection by flow cytometry and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The relationships among the LRT microbiota, the immune response, and the plasma metabolism profile were analyzed by Spearman's correlation analysis. IAV-MRSA coinfection showed significant weight loss and lung injury and significantly increased loads of IAV and MRSA in bronchoalveolar lavage fluid (BALF). Microbiome data showed that coinfection significantly increased the relative abundances of Enterococcus faecalis, Enterobacter hormaechei, Citrobacter freundii, and Klebsiella pneumoniae and decreased the relative abundances of Lactobacillus reuteri and Lactobacillus murinus. The percentages of CD4+/CD8+ T cells and B cells in the spleen; the levels of interleukin-9 (IL-9), interferon gamma (IFN-γ), tumor necrosis factor alpha (TNF-α), IL-6, and IL-8 in the lung; and the level of mevalonolactone in plasma were increased in IAV-MRSA-coinfected mice. L. murinus was positively correlated with lung macrophages and natural killer (NK) cells, negatively correlated with spleen B cells and CD4+/CD8+ T cells, and correlated with multiple plasma metabolites. Future research is needed to clarify whether L. murinus mediates or alters the severity of IAV-MRSA coinfection. IMPORTANCE The respiratory microbiome plays an important role in respiratory tract infections. In this study, we characterized the URT and LRT microbiota, the host immune response, and plasma metabolic profiles during IAV-MRSA coinfection and evaluated their correlations. We observed that IAV-MRSA coinfection induced severe lung injury and dysregulated host immunity and plasma metabolic profiles, as evidenced by the aggravation of lung pathological damage, the reduction of innate immune cells, the strong adaptation of the immune response, and the upregulation of mevalonolactone in plasma. L. murinus was strongly correlated with immune cells and plasma metabolites. Our findings contribute to a better understanding of the role of the host microbiome in respiratory tract infections and identified a key bacterial species, L. murinus, that may provide important references for the development of probiotic therapies.
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Affiliation(s)
- Qichao Chen
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing City, Jiangsu Province, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing City, Jiangsu Province, China
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing City, Jiangsu Province, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing City, Jiangsu Province, China
| | - Kaiying Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Jiangfeng Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yun Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- School of Public Health, China Medical University, Shenyang City, Liaoning Province, China
| | - Yanfeng Lin
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Jinhui Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Peihan Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Lang Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Leili Jia
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Juntao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Peng Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
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Finzer P, Küppers V, Griesser H. Dysbiotic Co-Factors in Cervical Cancer. How the Microbiome Influences the Development of Cervical Intraepithelial Neoplasia (CIN). Geburtshilfe Frauenheilkd 2023; 83:1017-1021. [PMID: 37588255 PMCID: PMC10427202 DOI: 10.1055/a-2044-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/20/2023] [Indexed: 08/18/2023] Open
Abstract
Human papillomavirus (HPV) infection is a necessary but not sufficient condition for the development of cervical cancer. The dysbiotic shift in the cervicovaginal microbiome appears to be a major co-factor in carcinogenesis. New analytical methods, such as next-generation sequencing (NGS), can be used to detect all of the vaginal microorganisms present and therefore identify individual therapeutic options. The relationship of bacterial vaginosis and carcinogenesis, as well as possible indications for the use of microbiome analysis, will be discussed.
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Affiliation(s)
- Patrick Finzer
- dus.ana Düsseldorf Analytik, Praxis für medizinische Mikrobiologie und Laboratoriumsmedizin, Düsseldorf, Germany
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Volkmar Küppers
- Zytologisches Labor, Dysplasie-Sprechstunde, Praxis für Frauenheilkunde & Geburtshilfe, Düsseldorf, Germany
| | - Henrik Griesser
- Fachabteilung Pathologie und Zytodiagnostik, Labor Dr. Wisplinghoff, Köln, Germany
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31
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Petrone JR, Rios Glusberger P, George CD, Milletich PL, Ahrens AP, Roesch LFW, Triplett EW. RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing. Front Microbiol 2023; 14:1201064. [PMID: 37547696 PMCID: PMC10402275 DOI: 10.3389/fmicb.2023.1201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis. Sequencing the near-entire rrn operon of bacteria and archaea enables the use of the universally conserved operon holding evolutionary polymorphisms for taxonomic resolution. Here, a reproducible and validated pipeline was developed, RRN-operon Enabled Species-level Classification Using EMU (RESCUE), to facilitate the sequencing of bacterial rrn operons and to support import into phyloseq. Benchmarking RESCUE showed that fully processed reads are now parallel or exceed the quality of Sanger, with median quality scores of approximately Q20+, using the R10.4 and Guppy SUP basecalling. The pipeline was validated through two complex mock samples, the use of multiple sample types, with actual Illumina data, and across four databases. RESCUE sequencing is shown to drastically improve classification to the species level for most taxa and resolves erroneous taxa caused by using short reads such as Illumina.
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32
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Contreras MJ, Leal K, Bruna P, Nuñez-Montero K, Goméz-Espinoza O, Santos A, Bravo L, Valenzuela B, Solis F, Gahona G, Cayo M, Dinamarca MA, Ibacache-Quiroga C, Zamorano P, Barrientos L. Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities. Front Microbiol 2023; 14:1197399. [PMID: 37538842 PMCID: PMC10395097 DOI: 10.3389/fmicb.2023.1197399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.
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Affiliation(s)
- María José Contreras
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Karla Leal
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Pablo Bruna
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Kattia Nuñez-Montero
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
- Biotechnology Research Center, Instituto Tecnológico de Costa Rica, Cártago, Costa Rica
| | - Olman Goméz-Espinoza
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Universitat Autònoma de Barcelona, Departament de Genètica i de Microbiologia, Institut Biotecnologia i de Biomedicina, Cerdanyola del Vallès, Barcelona, Spain
| | - León Bravo
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisco Solis
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Giovanni Gahona
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Mayra Cayo
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Leticia Barrientos
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
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Zhang W, Fan X, Shi H, Li J, Zhang M, Zhao J, Su X. Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats. Microbiol Spectr 2023; 11:e0056323. [PMID: 37102867 PMCID: PMC10269731 DOI: 10.1128/spectrum.00563-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is always considered only at the genus level; however, it has not been verified on a wide range of microbes yet. To fully explore the ability and potential of the 16S rRNA gene in microbial profiling, here, we propose Qscore, a comprehensive method to evaluate the performance of amplicons by integrating the amplification rate, multitier taxonomic annotation, sequence type, and length. Our in silico assessment by a "global view" of 35,889 microbe species across multiple reference databases summarizes the optimal sequencing strategy for 16S short reads. On the other hand, since microbes are unevenly distributed according to their habitats, we also provide the recommended configuration for 16 typical ecosystems based on the Qscores of 157,390 microbiomes in the Microbiome Search Engine (MSE). Detailed data simulation further proves that the 16S amplicons produced with Qscore-suggested parameters exhibit high precision in microbiome profiling, which is close to that of shotgun metagenomes under CAMI metrics. Therefore, by reconsidering the precision of 16S-based microbiome profiling, our work not only enables the high-quality reusability of massive sequence legacy that has already been produced but is also significant for guiding microbiome studies in the future. We have implemented the Qscore as an online service at http://qscore.single-cell.cn to parse the recommended sequencing strategy for specific habitats or expected microbial structures. IMPORTANCE 16S rRNA has long been used as a biomarker to identify distinct microbes from complex communities. However, due to the influence of the amplification region, sequencing type, sequence processing, and reference database, the accuracy of 16S rRNA has not been fully verified on a global range. More importantly, the microbial composition of different habitats varies greatly, and it is necessary to adopt different strategies according to the corresponding target microbes to achieve optimal analytical performance. Here, we developed Qscore, which evaluates the comprehensive performance of 16S amplicons from multiple perspectives, thus providing the best sequencing strategies for common ecological environments by using big data.
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Affiliation(s)
- Wenke Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Xiaoqian Fan
- Shouguang Hospital of Traditional Chinese Medicine, Weifang, China
| | - Haobo Shi
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Jian Li
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Mingqian Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Jin Zhao
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, China
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Stevens BM, Creed TB, Reardon CL, Manter DK. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Sci Rep 2023; 13:9323. [PMID: 37291169 PMCID: PMC10250467 DOI: 10.1038/s41598-023-36101-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Illumina MiSeq is the current standard for characterizing microbial communities in soil. The newer alternative, Oxford Nanopore Technologies MinION sequencer, is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (95% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the effects of platform, primers, and bioinformatics on mock community and agricultural soil samples using short MiSeq, and short and full-length MinION 16S rRNA amplicon sequencing. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9-90.5%; species: 70.9-85.2% Bray-Curtis similarity); however, the short MiSeq with error correction (DADA2) resulted in the correct estimate of mock community species richness and much lower alpha diversity for soils. Several filtering strategies were tested to improve these estimates with varying results. The sequencing platform also had a significant influence on the relative abundances of taxa with MiSeq resulting in significantly higher abundances Actinobacteria, Chloroflexi, and Gemmatimonadetes and lower abundances of Acidobacteria, Bacteroides, Firmicutes, Proteobacteria, and Verrucomicrobia compared to the MinION platform. When comparing agricultural soils from two different sites (Fort Collins, CO and Pendleton, OR), methods varied in the taxa identified as significantly different between sites. At all taxonomic levels, the full-length MinION method had the highest similarity to the short MiSeq method with DADA2 correction with 73.2%, 69.3%, 74.1%, 79.3%, 79.4%, and 82.28% of the taxa at the phyla, class, order, family, genus, and species levels, respectively, showing similar patterns in differences between the sites. In summary, although both platforms appear suitable for 16S rRNA microbial community composition, biases for different taxa may make the comparison between studies problematic; and even with a single study (i.e., comparing sites or treatments), the sequencing platform can influence the differentially abundant taxa identified.
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Affiliation(s)
- Bo Maxwell Stevens
- Water Management and Systems Research Unit, USDA ARS, Fort Collins, CO, 80526, USA
| | - Tim B Creed
- Soil Management and Sugar Beet Research Unit, USDA ARS, Fort Collins, CO, 80526, USA
| | - Catherine L Reardon
- Columbia Plateau Conservation Research Center, USDA ARS, Adams, OR, 97810, USA
| | - Daniel K Manter
- Soil Management and Sugar Beet Research Unit, USDA ARS, Fort Collins, CO, 80526, USA.
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Rutjens S, Vereecke N, Sauer J, Croubels S, Devreese M. Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur. Vet Res 2023; 54:45. [PMID: 37280708 DOI: 10.1186/s13567-023-01176-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg-1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg-1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.
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Affiliation(s)
- Sofie Rutjens
- Department of Pathobiology, Pharmacology and Zoological Medicine, Laboratory of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Nick Vereecke
- PathoSense BV, 2500, Lier, Belgium
- Department of Translational Physiology, Infectiology and Public Health, Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | | | - Siska Croubels
- Department of Pathobiology, Pharmacology and Zoological Medicine, Laboratory of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Mathias Devreese
- Department of Pathobiology, Pharmacology and Zoological Medicine, Laboratory of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
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Weber C, Dilthey A, Finzer P. The role of microbiome-host interactions in the development of Alzheimer´s disease. Front Cell Infect Microbiol 2023; 13:1151021. [PMID: 37333848 PMCID: PMC10272569 DOI: 10.3389/fcimb.2023.1151021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
Alzheimer`s disease (AD) is the most prevalent cause of dementia. It is often assumed that AD is caused by an aggregation of extracellular beta-amyloid and intracellular tau-protein, supported by a recent study showing reduced brain amyloid levels and reduced cognitive decline under treatment with a beta-amyloid-binding antibody. Confirmation of the importance of amyloid as a therapeutic target notwithstanding, the underlying causes of beta-amyloid aggregation in the human brain, however, remain to be elucidated. Multiple lines of evidence point towards an important role of infectious agents and/or inflammatory conditions in the etiology of AD. Various microorganisms have been detected in the cerebrospinal fluid and brains of AD-patients and have thus been hypothesized to be linked to the development of AD, including Porphyromonas gingivalis (PG) and Spirochaetes. Intriguingly, these microorganisms are also found in the oral cavity under normal physiological conditions, which is often affected by multiple pathologies like caries or tooth loss in AD patients. Oral cavity pathologies are mostly accompanied by a compositional shift in the community of oral microbiota, mainly affecting commensal microorganisms and referred to as 'dysbiosis'. Oral dysbiosis seems to be at least partly mediated by key pathogens such as PG, and it is associated with a pro-inflammatory state that promotes the destruction of connective tissue in the mouth, possibly enabling the translocation of pathogenic microbiota from the oral cavity to the nervous system. It has therefore been hypothesized that dysbiosis of the oral microbiome may contribute to the development of AD. In this review, we discuss the infectious hypothesis of AD in the light of the oral microbiome and microbiome-host interactions, which may contribute to or even cause the development of AD. We discuss technical challenges relating to the detection of microorganisms in relevant body fluids and approaches for avoiding false-positives, and introduce the antibacterial protein lactoferrin as a potential link between the dysbiotic microbiome and the host inflammatory reaction.
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Nakatsuji T, Brinton SL, Cavagnero KJ, O'Neill AM, Chen Y, Dokoshi T, Butcher AM, Osuoji OC, Shafiq F, Espinoza JL, Dupont CL, Hata TR, Gallo RL. Competition between skin antimicrobial peptides and commensal bacteria in type 2 inflammation enables survival of S. aureus. Cell Rep 2023; 42:112494. [PMID: 37167061 DOI: 10.1016/j.celrep.2023.112494] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023] Open
Abstract
During inflammation, the skin deploys antimicrobial peptides (AMPs) yet during allergic inflammation it becomes more susceptible to Staphylococcus aureus. To understand this contradiction, single-cell sequencing of Il4ra-/- mice combined with skin microbiome analysis reveals that lower production of AMPs from interleukin-4 receptor α (IL-4Rα) activation selectively inhibits survival of antibiotic-producing strains of coagulase-negative Staphylococcus (CoNS). Diminished AMPs under conditions of T helper type 2 (Th2) inflammation enable expansion of CoNS strains without antibiotic activity and increase Staphylococcus aureus (S. aureus), recapitulating the microbiome on humans with atopic dermatitis. This response is rescued in Camp-/- mice or after topical steroids, since further inhibition of AMPs enables survival of antibiotic-producing CoNS strains. In conditions of Th17 inflammation, a higher expression of host AMPs is sufficient to directly inhibit S. aureus survival. These results show that antimicrobials produced by the host and commensal bacteria each act to control S. aureus on the skin.
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Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Samantha L Brinton
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kellen J Cavagnero
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alan M O'Neill
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yang Chen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Tatsuya Dokoshi
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna M Butcher
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Olive C Osuoji
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Faiza Shafiq
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Josh L Espinoza
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Tissa R Hata
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA.
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Wagner GE, Dabernig-Heinz J, Lipp M, Cabal A, Simantzik J, Kohl M, Scheiber M, Lichtenegger S, Ehricht R, Leitner E, Ruppitsch W, Steinmetz I. Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance. J Clin Microbiol 2023; 61:e0163122. [PMID: 36988494 PMCID: PMC10117118 DOI: 10.1128/jcm.01631-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/17/2023] [Indexed: 03/30/2023] Open
Abstract
Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.
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Affiliation(s)
- Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Johanna Dabernig-Heinz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Michaela Lipp
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Adriana Cabal
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Jonathan Simantzik
- Medical and Life Sciences Faculty, Furtwangen University, Villingen-Schwenningen, Germany
| | - Matthias Kohl
- Medical and Life Sciences Faculty, Furtwangen University, Villingen-Schwenningen, Germany
| | - Martina Scheiber
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Sabine Lichtenegger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), Jena, Germany
- Friedrich Schiller University Jena, Institute of Physical Chemistry, Jena, Germany
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
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Zorz J, Li C, Chakraborty A, Gittins DA, Surcon T, Morrison N, Bennett R, MacDonald A, Hubert CRJ. SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis. ISME COMMUNICATIONS 2023; 3:33. [PMID: 37081077 PMCID: PMC10119094 DOI: 10.1038/s43705-023-00239-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.
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Affiliation(s)
- Jackie Zorz
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Daniel A Gittins
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Taylor Surcon
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Natasha Morrison
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, NS, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, NS, Canada
| | - Adam MacDonald
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, NS, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Szoboszlay M, Schramm L, Pinzauti D, Scerri J, Sandionigi A, Biazzo M. Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required. Microorganisms 2023; 11:microorganisms11030804. [PMID: 36985377 PMCID: PMC10059749 DOI: 10.3390/microorganisms11030804] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.
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Affiliation(s)
| | | | | | | | - Anna Sandionigi
- Department of Informatics, Systems and Communication, University of Milan Bicocca, 20126 Milan, Italy
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41
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Michishita R, Shimoda M, Furukawa S, Uehara T. Inoculation with black soldier fly larvae alters the microbiome and volatile organic compound profile of decomposing food waste. Sci Rep 2023; 13:4297. [PMID: 36922572 PMCID: PMC10017687 DOI: 10.1038/s41598-023-31388-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
The black soldier fly (BSF; Hermetia illucens) is used in sustainable processing of many types of organic waste. However, organic waste being decomposed by BSF produces strong odors, hindering more widespread application. The odor components and how they are produced have yet to be characterized. We found that digestion of food waste by BSF significantly alters the microbial flora, based on metagenomic analyses, and the odor components generated, as shown by thermal desorption gas chromatography mass spectrometry analysis. Inoculation with BSF significantly decreased production of volatile organic sulfur compounds (dimethyl disulfide and dimethyl trisulfide), which are known to be released during methionine and cysteine metabolism by Lactobacillus and Enterococcus bacteria. BSF inoculation significantly changed the abundance of Lactobacillus and Enterococcus and decreased microbial diversity overall. These findings may help in optimizing use of BSF for deodorization of composting food waste.
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Affiliation(s)
- Rena Michishita
- Division of Insect Sciences, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masami Shimoda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Seiichi Furukawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takuya Uehara
- Division of Insect Sciences, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan.
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Characterisation of the Gut Bacteria of Cultured and Wild Spiny Lobster Panulirus ornatus. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The commercial onshore aquaculture of the spiny lobster Panulirus ornatus, while in its infancy, has progressed rapidly from the enabling research that continues at the University of Tasmania. The development of lobster feeds, both fresh and manufactured, has been critical to the success of this emerging aquaculture sector. Fresh feeds derived from mussel represent the gold standard in terms of the growth performance of juvenile lobsters. Nonetheless, concerns regarding availability, sustainability, and potential biosecurity issues of fresh feeds highlight the importance of developing manufactured feeds for lobster aquaculture. Wild lobsters are assumed to have a balanced natural diet that allows for standard growth and development, and as such natural diets are often used as a reference for feed development. Similarly, the gut microbiota associated with a natural diet is assumed to reflect a healthy microbial assemblage. The aim of this study was to compare the microbiota of the hindgut and hepatopancreas of cultured P. ornatus fed with a commercial prawn pellet or mussel to that of wild spiny lobster juveniles. Gut samples were analysed using Oxford Nanopore 16S rRNA gene sequencing. Based on principal coordinate analysis, the gut bacteria of cultured lobsters were different from the wild juveniles. The core microbiota of the hindgut and hepatopancreas libraries were phyla Proteobacteria (Gamma, Alpha) and Bacteroidetes. Vibrio was the most dominant genus in both organs. The differences in bacterial relative abundance were mainly between cultured (pellet-, mussel-fed) and wild lobsters. In conclusion, bacteria in the cultured lobsters had significantly different profiles to that of the wild juveniles, indicating that current onshore aquaculture practices alter the gut microbiota. A number of different feeding and culture practices may be required if the aim of closed culture practices is to attain a gut microbiota in cultured animals that is representative of that found in wild spiny lobsters.
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Schwarz C, Mathieu J, Gomez JL, Miller MR, Tikhonova M, Nagaraja T, Alvarez PJJ. Unexpected finding of Fusobacterium varium as the dominant Fusobacterium species in cattle rumen: potential implications for liver abscess etiology and interventions. J Anim Sci 2023; 101:skad130. [PMID: 37104065 PMCID: PMC10195197 DOI: 10.1093/jas/skad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
Fusobacterium varium has been generally overlooked in cattle rumen microbiome studies relative to the presumably more abundant liver abscess-causing Fusobacterium necrophorum. However, F. varium was found to be more abundant in the rumen fluid of cattle and under culture conditions tailored to enrich F. necrophorum. Using near-full length 16S ribosomal ribonucleic acid sequencing, we demonstrate that F. varium grows under restrictive conditions commonly used to enumerate F. necrophorum, suggesting that previous F. necrophorum abundance assessment may have been inaccurate and that F. varium may be an underestimated member of the ruminal bacterial community. Fusobacterium varium were not as susceptible as F. necrophorum to in-feed antibiotics conventionally used in feedlots. Exposure to tylosin, the current gold standard for liver abscess reduction strategies in cattle, consistently hindered growth of the F. necrophorum strains tested by over 67% (P < 0.05) relative to the unexposed control. In contrast, F. varium strains were totally or highly resistant (0%-13% reduction in maximum yield, P < 0.05). Monensin, an ionophore antibiotic, had greater inhibitory activity against F. necrophorum than F. varium. Finally, preliminary genomic analysis of two F. varium isolates from the rumen revealed the presence of virulence genes related to those of pathogenic human F. varium isolates associated with active invasion of mammalian cells. The data presented here encourage further investigation into the ecological role of F. varium within the bovine rumen and potential role in liver abscess development, and proactive interventions.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| | | | - Megan R Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | | | - Tiruvoor.G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
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Beccaccioli M, Moricca C, Faino L, Reale R, Mineo M, Reverberi M. The Neolithic site "La Marmotta": DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood. Front Microbiol 2023; 14:1129983. [PMID: 37032892 PMCID: PMC10079079 DOI: 10.3389/fmicb.2023.1129983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The evaluation of biological degradation of waterlogged archeological wood is crucial to choose the conservative and protective treatments to be applied to the wooden material. The waterlogged environmental conditions are characterized by oxygen scarcity, only allowing the growth of adapted microbes capable to degrade the organic wooden material, mainly erosion bacteria and soft-rot fungi. In this work, we characterized and evaluated the biodegradation state and the microbial communities of wooden fragments preserved in storage tanks. These were preserved by waterlogging within the Neolithic village "La Marmotta," currently found under the Bracciano Lake (Lazio, Italy). Methods The waterlogged wood samples were first identified taxonomically with an optical microscope, also allowing an evaluation of their preservation state. The microbial community was then evaluated through the sequencing of Internal Transcribed Spacer sequences for fungi and 16S for bacteria with the Oxford Nanopore Technologies (ONT) MinION platform. Results The identified microbial community appears to be consistent with the waterlogged samples, as many bacteria attributable to the erosion of wood and ligninolytic fungi have been sequenced. Discussion The reported results highlight the first use of targeted metabarcoding by ONT applied to study the biodeterioration of waterlogged archeological wood.
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Affiliation(s)
- Marzia Beccaccioli
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
- *Correspondence: Marzia Beccaccioli,
| | - Claudia Moricca
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Luigi Faino
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Rita Reale
- Chemistry Applied to Restoration, A. Galli Academy, Via Petrarca, Como, Italy
| | - Mario Mineo
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Massimo Reverberi
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
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45
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The association between the respiratory tract microbiome and clinical outcomes in patients with COPD. Microbiol Res 2023; 266:127244. [DOI: 10.1016/j.micres.2022.127244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
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Lee AWT, Chan CTM, Wong LLY, Yip CY, Lui WT, Cheng KC, Leung JSL, Lee LK, Wong ITF, Ng TTL, Lao HY, Siu GKH. Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing. Front Microbiol 2023; 14:1164632. [PMID: 37125165 PMCID: PMC10133568 DOI: 10.3389/fmicb.2023.1164632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/14/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Microbes in the built environment have been implicated as a source of infectious diseases. Bacterial culture is the standard method for assessing the risk of exposure to pathogens in urban environments, but this method only accounts for <1% of the diversity of bacteria. Recently, full-length 16S rRNA gene analysis using nanopore sequencing has been applied for microbial evaluations, resulting in a rise in the development of long-read taxonomic tools for species-level classification. Regarding their comparative performance, there is, however, a lack of information. Methods Here, we aim to analyze the concordance of the microbial community in the urban environment inferred by multiple taxonomic classifiers, including ARGpore2, Emu, Kraken2/Bracken and NanoCLUST, using our 16S-nanopore dataset generated by MegaBLAST, as well as assess their abilities to identify culturable species based on the conventional culture results. Results According to our results, NanoCLUST was preferred for 16S microbial profiling because it had a high concordance of dominant species and a similar microbial profile to MegaBLAST, whereas Kraken2/Bracken, which had similar clustering results as NanoCLUST, was also desirable. Second, for culturable species identification, Emu with the highest accuracy (81.2%) and F1 score (29%) for the detection of culturable species was suggested. Discussion In addition to generating datasets in complex communities for future benchmarking studies, our comprehensive evaluation of the taxonomic classifiers offers recommendations for ongoing microbial community research, particularly for complex communities using nanopore 16S rRNA sequencing.
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Chen Q, Liu M, Lin Y, Wang K, Li J, Li P, Yang L, Jia L, Zhang B, Guo H, Li P, Song H. Topography of respiratory tract and gut microbiota in mice with influenza A virus infection. Front Microbiol 2023; 14:1129690. [PMID: 36910185 PMCID: PMC9992211 DOI: 10.3389/fmicb.2023.1129690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Influenza A virus (IAV)-induced dysbiosis may predispose to severe bacterial superinfections. Most studies have focused on the microbiota of single mucosal surfaces; consequently, the relationships between microbiota at different anatomic sites in IAV-infected mice have not been fully studied. Methods We characterized respiratory and gut microbiota using full-length 16S rRNA gene sequencing by Nanopore sequencers and compared the nasopharyngeal, oropharyngeal, lung and gut microbiomes in healthy and IAV-infected mice. Results The oropharyngeal, lung and gut microbiota of healthy mice were dominated by Lactobacillus spp., while nasopharyngeal microbiota were comprised primarily of Streptococcus spp. However, the oropharyngeal, nasopharyngeal, lung, and gut microbiota of IAV-infected mice were dominated by Pseudomonas, Escherichia, Streptococcus, and Muribaculum spp., respectively. Lactobacillus murinus was identified as a biomarker and was reduced at all sites in IAV-infected mice. The microbiota composition of lung was more similar to that of the nasopharynx than the oropharynx in healthy mice. Discussion These findings suggest that the main source of lung microbiota in mice differs from that of adults. Moreover, the similarity between the nasopharyngeal and lung microbiota was increased in IAV-infected mice. We found that IAV infection reduced the similarity between the gut and oropharyngeal microbiota. L. murinus was identified as a biomarker of IAV infection and may be an important target for intervention in post-influenza bacterial superinfections.
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Affiliation(s)
- Qichao Chen
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu Province, China.,Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, Jiangsu Province, China
| | - Yanfeng Lin
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Bei Zhang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu Province, China.,Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, Jiangsu Province, China
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu Province, China.,Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, Jiangsu Province, China
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
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48
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Lüth T, Graspeuntner S, Neumann K, Kirchhoff L, Masuch A, Schaake S, Lupatsii M, Tse R, Griesinger G, Trinh J, Rupp J. Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing. J Assist Reprod Genet 2022; 39:2659-2667. [PMID: 36223010 DOI: 10.1007/s10815-022-02628-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/25/2022] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis. METHODS Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference. RESULTS The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing. CONCLUSIONS Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.
| | - Kay Neumann
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Laura Kirchhoff
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Antonia Masuch
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Ronnie Tse
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Georg Griesinger
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
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