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Rajarajan A, Wolinska J, Walser JC, Dennis SR, Spaak P. Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance. MICROBIAL ECOLOGY 2023; 85:1578-1589. [PMID: 35486140 PMCID: PMC10167167 DOI: 10.1007/s00248-022-02011-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/08/2022] [Indexed: 05/10/2023]
Abstract
Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.
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Affiliation(s)
- Amruta Rajarajan
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institut Für Biologie, Freie Universität Berlin (FU), Berlin, Germany
| | | | - Stuart R Dennis
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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2
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Draft Genome Sequence of Agrobacterium radiobacter Strain MD22b, Isolated from a Grape Plant in Tajikistan. Microbiol Resour Announc 2023; 12:e0113122. [PMID: 36939329 PMCID: PMC10112236 DOI: 10.1128/mra.01131-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Agrobacterium radiobacter strain MD22b was isolated from infected fruit from Vatan Farm, a dekhkan farm in Yangibog (Tursunzade, Tajikistan). The 5.7-Mbp draft genome sequence presented here shares homology with chromosomes 1 and 2, as well as with the Ti plasmid from agrobacteria.
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3
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Pallerla SR, Van Dong D, Linh LTK, Van Son T, Quyen DT, Hoan PQ, Trung NT, The NT, Rüter J, Boutin S, Nurjadi D, Sy BT, Kremsner PG, Meyer CG, Song LH, Velavan TP. Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting. Ann Clin Microbiol Antimicrob 2022; 21:39. [PMID: 36064402 PMCID: PMC9443622 DOI: 10.1186/s12941-022-00530-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022] Open
Abstract
Aim The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise. Methods DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics. Results Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30). Conclusion Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00530-6.
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Affiliation(s)
- Srinivas Reddy Pallerla
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Do Van Dong
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Thi Kieu Linh
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Trinh Van Son
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Dao Thanh Quyen
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Phan Quoc Hoan
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Ngo Tat Trung
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Nguyen Trong The
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Bui Tien Sy
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Peter G Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Christian G Meyer
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam. .,108 Military Central Hospital, Hanoi, Vietnam.
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany. .,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.
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4
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Lee SH. A Routine Sanger Sequencing Target Specific Mutation Assay for SARS-CoV-2 Variants of Concern and Interest. Viruses 2021; 13:2386. [PMID: 34960655 PMCID: PMC8706074 DOI: 10.3390/v13122386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/20/2022] Open
Abstract
As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have a potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein, along with certain mutations in other regions within the S protein as specific variants, in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.
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Affiliation(s)
- Sin Hang Lee
- Affiliation Milford Molecular Diagnostics Laboratory, 2044 Bridgeport Avenue, Milford, CT 06460, USA
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Establishment and assessment of an amplicon sequencing method targeting the 16S-ITS-23S rRNA operon for analysis of the equine gut microbiome. Sci Rep 2021; 11:11884. [PMID: 34088956 PMCID: PMC8178347 DOI: 10.1038/s41598-021-91425-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/24/2021] [Indexed: 02/08/2023] Open
Abstract
Microbial communities are commonly studied by using amplicon sequencing of part of the 16S rRNA gene. Sequencing of the full-length 16S rRNA gene can provide higher taxonomic resolution and accuracy. To obtain even higher taxonomic resolution, with as few false-positives as possible, we assessed a method using long amplicon sequencing targeting the rRNA operon combined with a CCMetagen pipeline. Taxonomic assignment had > 90% accuracy at the species level in a mock sample and at the family level in equine fecal samples, generating similar taxonomic composition as shotgun sequencing. The rRNA operon amplicon sequencing of equine fecal samples underestimated compositional percentages of bacterial strains containing unlinked rRNA genes by a fourth to a third, but unlinked rRNA genes had a limited effect on the overall results. The rRNA operon amplicon sequencing with the A519F + U2428R primer set was able to detect some kind of archaeal genomes such as Methanobacteriales and Methanomicrobiales, whereas full-length 16S rRNA with 27F + 1492R could not. Therefore, we conclude that amplicon sequencing targeting the rRNA operon captures more detailed variations of equine microbiota.
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Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon. BIOLOGY 2020; 9:biology9120440. [PMID: 33287185 PMCID: PMC7761764 DOI: 10.3390/biology9120440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 11/18/2022]
Abstract
Simple Summary Exploring the genomic changes that organisms have undergone to adapt to their specific environment is one of the most important processes in ecology and evolutionary biology. Here, we found that almost all rRNA operon-unlinked bacteria are symbiotic bacteria, which could be evidence of specific selective pressures in symbionts like genome reduction. This is meaningful and suggests that not only does the copy number variation of the rRNA operon sensitively respond to the bacterial lifestyle, but structural modification can also strongly reflect adaptation to the surrounding environmental conditions. Abstract Ribosomal RNA is an indispensable molecule in living organisms that plays an essential role in protein synthesis. Especially in bacteria, 16S, 23S, and 5S rRNAs are usually co-transcribed as operons. Despite the positive effects of rRNA co-transcription on growth and reproduction rate, a recent study revealed that bacteria with unlinked rRNA operons are more widespread than expected. However, it is still unclear why the rRNA operon is broken. Here, we explored rRNA operon linkage status in 15,898 bacterial genomes and investigated whether they have common features or lifestyles; 574 genomes were found to have unlinked rRNA operons and tended to be phylogenetically conserved. Most of them were symbionts and showed enhanced symbiotic genomic features such as reduced genome size and high adenine–thymine (AT) content. In an eggNOG-mapper analysis, they were also found to have significantly fewer genes than rRNA operon-linked bacteria in the “transcription” and “energy production and conversion in metabolism” categories. These genomes also tend to decrease RNases related to the synthesis of ribosomes and tRNA processing. Based on these results, the disruption of the rRNA operon seems to be one of the tendencies associated with the characteristics of bacteria requiring a low dynamic range.
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Unlinked rRNA genes are widespread among bacteria and archaea. ISME JOURNAL 2019; 14:597-608. [PMID: 31712737 DOI: 10.1038/s41396-019-0552-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023]
Abstract
Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.
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Sánchez J, Vegas C, Zavaleta AI, Esteve-Zarzoso B. Predominance of Lactobacillus plantarum Strains in Peruvian Amazonian Fruits. Pol J Microbiol 2019; 68:127-137. [PMID: 31050261 PMCID: PMC7256758 DOI: 10.21307/pjm-2019-015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2019] [Indexed: 12/22/2022] Open
Abstract
The objective of this research was the identification and characterization of lactic acid bacteria (LAB) isolated from Peruvian Amazonian fruits. Thirty-seven isolates were obtained from diverse Amazonian fruits. Molecular characterization of the isolates was performed by ARDRA, 16S-23S ITS RFLP and rep-PCR using GTG5 primers. Identification was carried out by sequencing the 16S rDNA gene. Phenotypic characterization included nutritional, physiological and antimicrobial resistance tests. Molecular characterization by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and 16S-23S ITS RFLP resulted in four restriction profiles while GTG5 analysis showed 14 banding patterns. Based on the 16S rDNA gene sequence, the isolates were identified as Lactobacillus plantarum (75.7%), Weissella cibaria (13.5%), Lactobacillus brevis (8.1%), and Weissella confusa (2.7%). Phenotypic characterization showed that most of the isolates were homofermentative bacilli, able to ferment glucose, maltose, cellobiose, and fructose and grow in a broad range of temperatures and pH. The isolates were highly susceptible to ampicillin, amoxicillin, clindamycin, chloramphenicol, erythromicyn, penicillin, and tetracycline and showed great resistance to kanamycin, gentamycin, streptomycin, sulfamethoxazole/trimethoprim, and vancomycin. No proteolytic or amylolytic activity was detected. L. plantarum strains produce lactic acid in higher concentrations and Weissella strains produce exopolymers only from sucrose. Molecular methods allowed to accurately identify the LAB isolates from the Peruvian Amazonian fruits, while phenotypic methods provided information about their metabolism, physiology and other characteristics that may be useful in future biotechnological processes. Further research will focus especially on the study of L. plantarum strains.
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Affiliation(s)
- Johanna Sánchez
- Laboratorio de Biología Molecular, Facultad de Farmacia y Bioquímica, Universidad Nacional Mayor de San Marcos , Lima , Perú
| | - Carlos Vegas
- Laboratorio de Biología Molecular, Facultad de Farmacia y Bioquímica, Universidad Nacional Mayor de San Marcos , Lima , Perú
| | - Amparo Iris Zavaleta
- Laboratorio de Biología Molecular, Facultad de Farmacia y Bioquímica, Universidad Nacional Mayor de San Marcos , Lima , Perú
| | - Braulio Esteve-Zarzoso
- Departament de Bioquímica i Biotecnologia, Facultat d' Enologia, Universitat Rovira i Virgili , Tarragona , Spain
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LANDRIEL SOLEDADCAMINATA, CASTILLO JULIETAD, TABOGA OSCARA, FERRAROTTI SUSANAA, GOTTLIEB ALEXANDRAM, COSTA HERNÁN. Molecular identification of a cyclodextrin glycosyltransferase-producing microorganism and phylogenetic assessment of enzymatic activities. AN ACAD BRAS CIENC 2019; 91:e20180568. [DOI: 10.1590/0001-3765201920180568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/10/2019] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - OSCAR A. TABOGA
- Instituto Nacional de Tecnología Agropecuaria (IABIMO-INTA-CONICET), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
| | | | - ALEXANDRA M. GOTTLIEB
- Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
| | - HERNÁN COSTA
- Universidad Nacional de Luján, Argentina; Universidad Nacional de Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
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Cuscó A, Catozzi C, Viñes J, Sanchez A, Francino O. Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon. F1000Res 2018; 7:1755. [PMID: 30815250 PMCID: PMC6372929 DOI: 10.12688/f1000research.16817.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples often contain DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to assess long-amplicon PCR-based approaches for assigning taxonomy at the genus and species level. We use Nanopore sequencing with two different markers: full-length 16S rRNA (~1,500 bp) and the whole rrn operon (16S rRNA-ITS-23S rRNA; 4,500 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities (HM-783D, Bei Resources; D6306, ZymoBIOMICS™) and two pools of low-biomass samples (dog skin from either the chin or dorsal back), using the MinION™ sequencer 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using the WIMP workflow on EPI2ME or Minimap2 software with rrn database. Results: The full-length 16S rRNA and the rrn operon were used to retrieve the microbiota composition at the genus and species level from the bacterial isolate, mock communities and complex skin samples. For the Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the rrn operon marker, and in ~68% of the cases with the 16S rRNA gene. In both skin microbiota samples, we detected many species with an environmental origin. In chin, we found different Pseudomonas species in high abundance, whereas in dorsal skin there were more taxa with lower abundances. Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, using the rrn operon would be the best choice.
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Affiliation(s)
- Anna Cuscó
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Carlotta Catozzi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Joaquim Viñes
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Armand Sanchez
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
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Cuscó A, Catozzi C, Viñes J, Sanchez A, Francino O. Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon. F1000Res 2018; 7:1755. [PMID: 30815250 PMCID: PMC6372929 DOI: 10.12688/f1000research.16817.2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.
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Affiliation(s)
- Anna Cuscó
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Carlotta Catozzi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Joaquim Viñes
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Armand Sanchez
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
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Schanche M, Avershina E, Dotterud C, Øien T, Storrø O, Johnsen R, Rudi K. High-Resolution Analyses of Overlap in the Microbiota Between Mothers and Their Children. Curr Microbiol 2015; 71:283-90. [PMID: 26044992 DOI: 10.1007/s00284-015-0843-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/18/2015] [Indexed: 12/01/2022]
Abstract
Understanding the transmission of the human microbiota from mother to child is of major importance. Although we are gaining knowledge using 16S rRNA gene analyses, the resolution of this gene is not sufficient to determine transmission patterns. We therefore developed an Illumina deep sequencing approach targeting the 16-23S rRNA Internal Transcribed Spacer (ITS) for high-resolution microbiota analyses. Using this approach, we analyzed the composition and potential mother to child transmission patterns of the microbiota (milk and stool) in a longitudinal cohort of 20 mother/child pairs. Our results show overlap in the infant stool microbiota with both mother's milk and stool, and that the overlap with stool increases with age. We found an Operational Taxonomic Unit resembling Streptococcus gordonii as the most widespread colonizer of both mothers and their children. In conclusion, the increased resolution of 16-23S rRNA ITS deep sequencing revealed new knowledge about potential transmission patterns of human-associated bacteria.
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Affiliation(s)
- Melissa Schanche
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
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Kaewklom S, Chueakhalm W, Suthirawut S, Aunpad R. Development of a Novel PCR Primer to Differentiate and IdentifyBacillus subtilisand Closely Related Species Isolated from Thai Fermented Foods. FOOD BIOTECHNOL 2014. [DOI: 10.1080/08905436.2014.964252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Yadegar A, Alebouyeh M, Lawson AJ, Mirzaei T, Nazemalhosseini Mojarad E, Zali MR. Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene. World J Microbiol Biotechnol 2014; 30:1909-17. [PMID: 24493015 DOI: 10.1007/s11274-014-1615-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/27/2014] [Indexed: 01/21/2023]
Abstract
Phenotypic identification of non-pylori Helicobacter species has always been problematic and time-consuming in comparison with many other bacteria. We developed a rapid two-step identification assay based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 23S rRNA gene for differentiating between non-pylori Helicobacter species. A new genus-specific primer pair based on all available complete and partial 23S rRNA sequences of Helicobacter species was designed. In silico restriction analysis of variable regions of the 23S rRNA gene suggested SmaI and HindIII endonucleases would provide a good level of differentiation. Analysis of the obtained 23S rRNA RFLP patterns divided all Helicobacter study strains into three species groups (groups A-C) and 12 unique restriction patterns. Wolinella succinogenes also gave a unique pattern. Our proposed PCR-RFLP method was found to be as a valuable tool for routine identification of non-pylori Helicobacter species from human or animal samples.
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Affiliation(s)
- Abbas Yadegar
- Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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