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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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2
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Eisenhofer R, Wright S, Weyrich L. Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PeerJ 2024; 12:e16770. [PMID: 38440408 PMCID: PMC10911074 DOI: 10.7717/peerj.16770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/16/2023] [Indexed: 03/06/2024] Open
Abstract
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.
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Affiliation(s)
| | - Sterling Wright
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
| | - Laura Weyrich
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
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Álvarez Narváez S, Beaudry MS, Norris CG, Bartlett PB, Glenn TC, Sanchez S. Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture. Animals (Basel) 2024; 14:445. [PMID: 38338088 PMCID: PMC10854943 DOI: 10.3390/ani14030445] [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: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the current microbiome sequencing methods has hampered the identification of specific bacterial changes associated with GITDs in horses. Here, we have compared TEHC, a new approach for 16S rRNA gene selection and sequencing, with conventional 16S rRNA gene amplicon sequencing for the characterization of the equine fecal microbiome. Both sequencing approaches were used to determine the fecal microbiome of four adult horses and one commercial mock microbiome. Our results show that TEHC yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing when the same number of reads were used in the analysis. This translated into a deeper and more accurate characterization of the fecal microbiome when the samples were sequenced with TEHC according to the relative abundance analysis. Alpha and beta diversity metrics corroborated these findings and demonstrated that the microbiome of the fecal samples was significantly richer when sequenced with TEHC compared to 16S amplicon sequencing. Altogether, our study suggests that the TEHC strategy provides a more extensive characterization of the fecal microbiome of horses than the current alternative based on the PCR amplification of a portion of the 16S rRNA gene.
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Affiliation(s)
- Sonsiray Álvarez Narváez
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Megan S. Beaudry
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA; (M.S.B.); (T.C.G.)
| | - Connor G. Norris
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Paula B. Bartlett
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Travis C. Glenn
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA; (M.S.B.); (T.C.G.)
| | - Susan Sanchez
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
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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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Ospino MC, Engel K, Ruiz-Navas S, Binns WJ, Doxey AC, Neufeld JD. Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples. ISME COMMUNICATIONS 2024; 4:ycae024. [PMID: 38500705 PMCID: PMC10945365 DOI: 10.1093/ismeco/ycae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific amplification have been reported from MDA-amplified samples, the impact of MDA on metagenomic datasets is not well understood. We compared three MDA methods (i.e. bulk MDA, emulsion MDA, and primase MDA) for metagenomic analysis of two DNA template concentrations (approx. 1 and 100 pg) derived from a microbial community standard "mock community" and two low biomass environmental samples (i.e. borehole fluid and groundwater). We assessed the impact of MDA on metagenome-based community composition, assembly quality, functional profiles, and binning. We found amplification bias against high GC content genomes but relatively low nonspecific amplification such as chimeras, artifacts, or contamination for all MDA methods. We observed MDA-associated representational bias for microbial community profiles, especially for low-input DNA and with the primase MDA method. Nevertheless, similar taxa were represented in MDA-amplified libraries to those of unamplified samples. The MDA libraries were highly fragmented, but similar functional profiles to the unamplified libraries were obtained for bulk MDA and emulsion MDA at higher DNA input and across these MDA libraries for the groundwater sample. Medium to low-quality bins were possible for the high input bulk MDA metagenomes for the most simple microbial communities, borehole fluid, and mock community. Although MDA-based amplification should be avoided, it can still reveal meaningful taxonomic and functional information from samples with extremely low DNA concentration where direct metagenomics is otherwise impossible.
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Affiliation(s)
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Santiago Ruiz-Navas
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - W Jeffrey Binns
- Safety and Technical Research, Nuclear Waste Management Organization of Canada, Toronto, Ontario M4T 2S3, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Baba H, Kuroda M, Sekizuka T, Kanamori H. Highly sensitive detection of antimicrobial resistance genes in hospital wastewater using the multiplex hybrid capture target enrichment. mSphere 2023; 8:e0010023. [PMID: 37222510 PMCID: PMC10449491 DOI: 10.1128/msphere.00100-23] [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: 02/27/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023] Open
Abstract
Wastewater can be useful in monitoring the spread of antimicrobial resistance (AMR) within a hospital. The abundance of antibiotic resistance genes (ARGs) in hospital effluent was assessed using metagenomic sequencing (mDNA-seq) and hybrid capture (xHYB). mDNA-seq analysis and subsequent xHYB targeted enrichment were conducted on two effluent samples per month from November 2018 to May 2021. Reads per kilobase per million (RPKM) values were calculated for all 1,272 ARGs in the constructed database. The monthly numbers of patients with presumed extended-spectrum β-lactamase (ESBL)-producing and metallo-β-lactamase (MBL)-producing bacteria, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE) were compared with the monthly RPKM values of blaCTX-M, blaIMP, mecA, vanA, and vanB by xHYB. The average RPKM value for all ARGs detected by xHYB was significantly higher than that of mDNA-seq (665, 225, and 328, respectively, and P < 0.05). The average number of patients with ESBL producers and RPKM values of blaCTX-M-1 genes in 2020 were significantly higher than that in 2019 (17 and 13 patients per month and 921 vs 232 per month, respectively, both P < 0.05). The average numbers of patients with MBL-producers, MRSA, and VRE were 1, 28, and 0 per month, respectively, while the average RPKM values of blaIMP, mecA, vanA, and vanB were 6,163, 6, 0, and 126 per month, respectively. Monitoring ARGs in hospital effluent using xHYB was found to be more useful than conventional mDNA-seq in detecting ARGs including blaCTX-M, blaIMP, and vanB, which are important for infection control.IMPORTANCEEnvironmental ARGs play a crucial role in the emergence and spread of AMR that constitutes a significant global health threat. One major source of ARGs is effluent from healthcare facilities, where patients are frequently administered antimicrobials. Culture-independent methods, including metagenomics, can detect environmental ARGs carried by non-culturable bacteria and extracellular ARGs. mDNA-seq is one of the most comprehensive methods for environmental ARG surveillance; however, its sensitivity is insufficient for wastewater surveillance. This study demonstrates that xHYB appropriately monitors ARGs in hospital effluent for sensitive identification of nosocomial AMR dissemination. Correlations were observed between the numbers of inpatients with antibiotic-resistant bacteria and the ARG RPKM values in hospital effluent over time. ARG surveillance in hospital effluent using the highly sensitive and specific xHYB method could improve our understanding of the emergence and spread of AMR within a hospital.
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Affiliation(s)
- Hiroaki Baba
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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Yadav R, Khare P. Dissipation kinetics of chlorpyrifos and 3,5,6 trichloro-2-pyridinol under vegetation of different aromatic grasses: Linkage with enzyme kinetics and microbial community of soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130960. [PMID: 36860046 DOI: 10.1016/j.jhazmat.2023.130960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The dissipation of chlorpyrifos (CP) and its hydrolytic metabolite 3,5,6-trichloro-2-pyridinol (TCP) in the soil is crucial for safe agriculture. However, there is still lacking relevant information about its dissipation under different vegetation for remediation purposes. In the present study, evaluation of dissipation of CP and TCP in non-planted and planted soil with different cultivars of three types of aromatic grass viz Cymbopogon martinii (Roxb. Wats), Cymbopogon flexuosus, and Chrysopogon zizaniodes (L.) Nash was examined in light of soil enzyme kinetics, microbial communities, and root exudation. Results revealed that the dissipation of CP was well-fitted into a single first-order exponential model (SFO). A significant reduction in the half-life (DT50) of CP was observed in planted soil (30-63 days) than in non-planted soil (95 days). The presence of TCP in all soil samples was observed. The three types of the inhibitory effect of CP i.e. linear mixed inhibition (increase in enzyme-substrate affinity (Km) and decrease in enzyme pool (Vmax), un-competitive inhibition (decrease in Km and Vmax), and simple competitive inhibition were observed on soil enzymes involved in mineralization of carbon, nitrogen, phosphorus, and sulfur. The improvement in the enzyme pool (Vmax) was observed in planted soil. Streptomyces, Clostridium, Kaistobacter, Planctomyces, and Bacillus were the dominant genera in CP stress soil. CP contamination in soil demonstrated a reduction of richness in microbial diversity and enhancement of functional gene family related to cellular process, metabolism, genetic, and environmental information processing. Among all the cultivars, C. flexuosus cultivars demonstrated a higher dissipation rate of CP along with more root exudation.
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Affiliation(s)
- Ranu Yadav
- Crop Production and Protection Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Puja Khare
- Crop Production and Protection Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Lemke M, DeSalle R. The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability. MICROBIAL ECOLOGY 2023; 85:781-795. [PMID: 36826587 PMCID: PMC10156817 DOI: 10.1007/s00248-023-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 05/04/2023]
Abstract
Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
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Affiliation(s)
- Michael Lemke
- Department of Biology, University of Illinois at Springfield, Springfield, IL, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Carrasco-Espinosa K, Avitia M, Barrón-Sandoval A, Abbruzzini TF, Salazar Cabrera UI, Arroyo-Lambaer D, Uscanga A, Campo J, Benítez M, Wegier A, Rosell JA, Reverchon F, Hernández G, Boege K, Escalante AE. Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems. Microorganisms 2022; 10:microorganisms10091763. [PMID: 36144367 PMCID: PMC9504970 DOI: 10.3390/microorganisms10091763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the central role of microorganisms in soil fertility, little understanding exists regarding the impact of management practices and soil microbial diversity on soil processes. Strong correlations among soil microbial composition, management practices, and microbially mediated processes have been previously shown. However, limited integration of the different parameters has hindered our understanding of agroecosystem functioning. Multivariate analyses of these systems allow simultaneous evaluation of the parameters and can lead to hypotheses on the microbial groups involved in specific nutrient transformations. In the present study, using a multivariate approach, we investigated the effect of microbial composition (16SrDNA sequencing) and soil properties in carbon mineralization (CMIN) (BIOLOG™, Hayward, CA, USA) across different management categories on coffee agroecosystems in Mexico. Results showed that (i) changes in soil physicochemical variables were related to management, not to region, (ii) microbial composition was associated with changes in management intensity, (iii) specific bacterial groups were associated with different management categories, and (iv) there was a broader utilization range of carbon sources in non-managed plots. The identification of specific bacterial groups, management practices, and soil parameters, and their correlation with the utilization range of carbon sources, presents the possibility to experimentally test hypotheses on the interplay of all these components and further our understanding of agroecosystem functioning and sustainable management.
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Affiliation(s)
- Karen Carrasco-Espinosa
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Morena Avitia
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Thalita F. Abbruzzini
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ulises Isaac Salazar Cabrera
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Denise Arroyo-Lambaer
- Laboratorio de Restauración Ecológica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Adriana Uscanga
- Laboratorio de Restauración Ecológica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Julio Campo
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Julieta A. Rosell
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Pátzcuaro 91070, Mexico
| | - Gerardo Hernández
- Centro Agroecológico del Café A.C. Clúster Biomimic-Inecol, Xalapa Enríquez Centro, Veracruz 91000, Mexico
| | - Karina Boege
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Correspondence:
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10
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Zheng X, Zhu Q, Qin M, Zhou Z, Liu C, Wang L, Shi F. The Role of Feeding Characteristics in Shaping Gut Microbiota Composition and Function of Ensifera (Orthoptera). INSECTS 2022; 13:719. [PMID: 36005344 PMCID: PMC9409189 DOI: 10.3390/insects13080719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Feeding habits were the primary factor affecting the gut bacterial communities in Ensifera. However, the interaction mechanism between the gut microbiota and feeding characteristics is not precisely understood. Here, the gut microbiota of Ensifera with diverse feeding habits was analyzed by shotgun metagenomic sequencing to further clarify the composition and function of the gut microbiota and its relationship with feeding characteristics. Our results indicate that under the influence of feeding habits, the gut microbial communities of Ensifera showed specific characteristics. Firstly, the gut microbial communities of the Ensifera with different feeding habits differed significantly, among which the gut microbial diversity of the herbivorous Mecopoda niponensis was the highest. Secondly, the functional genes related to feeding habits were in high abundance. Thirdly, the specific function of the gut microbial species in the omnivorous Gryllotalpa orientalis showed that the more diverse the feeding behavior of Ensifera, the worse the functional specificity related to the feeding characteristics of its gut microbiota. However, feeding habits were not the only factors affecting the gut microbiota of Ensifera. Some microorganisms' genes, whose functions were unrelated to feeding characteristics but were relevant to energy acquisition and nutrient absorption, were detected in high abundance. Our results were the first to report on the composition and function of the gut microbiota of Ensifera based on shotgun metagenomic sequencing and to explore the potential mechanism of the gut microbiota's association with diverse feeding habits.
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Affiliation(s)
- Xiang Zheng
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology Co., Ltd., Baoding 071051, China
| | - Qidi Zhu
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Meng Qin
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology Co., Ltd., Baoding 071051, China
- College of Life Sciences, Hebei Agricultural University, Baoding 071001, China
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunmao Liu
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology Co., Ltd., Baoding 071051, China
| | - Liyuan Wang
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology Co., Ltd., Baoding 071051, China
| | - Fuming Shi
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
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11
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Chakoory O, Comtet-Marre S, Peyret P. RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties. NAR Genom Bioinform 2022; 4:lqac070. [PMID: 36159175 PMCID: PMC9492272 DOI: 10.1093/nargab/lqac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Metagenomic classifiers are widely used for the taxonomic profiling of metagenomics data and estimation of taxa relative abundance. Small subunit rRNA genes are a gold standard for phylogenetic resolution of microbiota, although the power of this marker comes down to its use as full-length. We aimed at identifying the tools that can efficiently lead to taxonomic resolution down to the species level. To reach this goal, we benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then compiled the best tools (BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2’s Sklearn classifier) to build a pipeline called RiboTaxa. Using metagenomics datasets, RiboTaxa gave the best results compared to other tools (i.e. Kraken2, Centrifuge, METAXA2, phyloFlash, SPINGO, BLCA, MEGAN) with precise taxonomic identification and relative abundance description without false positive detection (F-measure of 100% and 83.7% at genus level and species level, respectively). Using real datasets from various environments (i.e. ocean, soil, human gut) and from different approaches (e.g. metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not discerned by current bioinformatics analysis opening new biological perspectives in human and environmental health.
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Affiliation(s)
- Oshma Chakoory
- Université Clermont Auvergne, INRAE, MEDIS , F-63000 Clermont-Ferrand, France
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDIS , F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDIS , F-63000 Clermont-Ferrand, France
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12
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Lugli GA, Ventura M. A breath of fresh air in microbiome science: shallow shotgun metagenomics for a reliable disentangling of microbial ecosystems. MICROBIOME RESEARCH REPORTS 2022; 1:8. [PMID: 38045646 PMCID: PMC10688782 DOI: 10.20517/mrr.2021.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 12/05/2023]
Abstract
Next-generation sequencing technologies allow accomplishing massive DNA sequencing, uncovering the microbial composition of many different ecological niches. However, the various strategies developed to profile microbiomes make it challenging to retrieve a reliable classification that is able to compare metagenomic data of different studies. Many limitations have been overcome thanks to shotgun sequencing, allowing a reliable taxonomic classification of microbial communities at the species level. Since numerous bioinformatic tools and databases have been implemented, the sequencing methodology is only the first of many choices to make for classifying metagenomic data. Here, we discuss the importance of choosing a reliable methodology to achieve consistent information in uncovering microbiomes.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
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13
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Dery KJ, Kupiec-Weglinski JW, Dong TS. The human microbiome in transplantation: the past, present, and future. Curr Opin Organ Transplant 2021; 26:595-602. [PMID: 34545840 DOI: 10.1097/mot.0000000000000922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Over the past 20 years, DNA sequencing technology has transformed human microbiome research from identity characterizations to metagenomics approaches that reveal how microbials correlate with human health and disease. New studies are showing unprecedented opportunity for deep characterization of the human microbial ecosystem, with benefits to the field of organ transplantation. RECENT FINDINGS In the present review, we focus on past milestones of human-associated microbiota research, paying homage to microbiota pioneers. We highlight the role of sequencing efforts to provide insights beyond taxonomic identification. Recent advances in microbiome technology is now integrating high-throughput datasets, giving rise to multi'omics - a comprehensive assessment modeling dynamic biologic networks. Studies that show benefits and mechanisms in peritransplant antibiotic (Abx)-conditioned recipients are reviewed. We describe how next-generation microbial sequencing has the potential to combine with new technologies like phage therapy (PT) to translate into life-saving therapeutics. SUMMARY The study of the microbiome is advancing the field of transplantation by enhancing our knowledge of precision medicine. Sequencing technology has allowed the use of the microbiome as a biomarker to risk stratify patients. Further research is needed to better understand how microbiomes shape transplantation outcomes while informing immune cell - tissue crosstalk platforms.
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Affiliation(s)
- Kenneth J Dery
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation
| | - Jerzy W Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation
| | - Tien S Dong
- Department of Medicine, Vatche & Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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14
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Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Mol Ecol Resour 2021; 22:1100-1119. [PMID: 34569723 DOI: 10.1111/1755-0998.13517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/01/2022]
Abstract
Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.
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Affiliation(s)
- Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Kerry A Cobb
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Daniel M Portik
- California Academy of Sciences, San Francisco, California, USA
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA.,Department of Biological Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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15
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Beaudry MS, Thomas JC, Baptista RP, Sullivan AH, Norfolk W, Devault A, Enk J, Kieran TJ, Rhodes OE, Perry-Dow KA, Rose LJ, Bayona-Vásquez NJ, Oladeinde A, Lipp EK, Sanchez S, Glenn TC. Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environ Microbiol 2021; 23:7523-7537. [PMID: 34519156 DOI: 10.1111/1462-2920.15767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.
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Affiliation(s)
- Megan S Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Amanda H Sullivan
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - William Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Alison Devault
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Olin E Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA.,Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - K Allison Perry-Dow
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura J Rose
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Division of Natural Science and Mathematics, Oxford College, Emory University, Oxford, GA, 30054, USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
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