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Fischer MT, Xue KS, Costello EK, Dvorak M, Robaczewska A, Raboisson G, Caty SN, Relman DA, O'Connell LA. Effects of parental care on skin microbial community composition in poison frogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612488. [PMID: 39314287 PMCID: PMC11419107 DOI: 10.1101/2024.09.11.612488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects. Early exposure to microbes can have lasting influences on the assembly and functionality of the host's microbiota, leaving a life-long imprint on host health and disease. Studies of the role played by parental care in microbial acquisition have primarily focused on humans and hosts with agricultural relevance. Anuran vertebrates offer the opportunity to examine microbial community composition across life stages as a function of parental investment. In this study, we investigate vertical transmission of microbiota during parental care in a poison frog (Family Dendrobatidae), where fathers transport their offspring piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of the embryo begins after hatching from the vitelline envelope, emphasizing its potential role as microbial barrier during early development. Using a laboratory cross-foster experiment, we demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts the microbial skin communities of tadpoles in an ecologically relevant setting, we sampled frogs and tadpoles of sympatric species that do or do not exhibit tadpole transport in their natural habitat. We found more diverse microbial communities associated with tadpoles of transporting species compared to a non-transporting frog. However, we detected no difference in the degree of similarity between adult and tadpole skin microbiotas, based on whether the frog species exhibits transporting behavior or not. Using a field experiment, we confirmed that tadpole transport can result in the persistent colonization of tadpoles by isolated microbial taxa associated with the caregiver's skin, albeit often at low prevalence. This is the first study to describe vertical transmission of skin microbes in anuran amphibians, showing that offspring transport may serve as a mechanism for transmission of parental skin microbes. Overall, these findings provide a foundation for further research on how vertical transmission in this order impacts host-associated microbiota and physiology.
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Bischof PSP, Bartolomaeus TUP, Löber U, Bleidorn C. Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies. MICROBIAL ECOLOGY 2024; 87:91. [PMID: 38960913 PMCID: PMC11222186 DOI: 10.1007/s00248-024-02403-1] [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: 01/18/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.
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Affiliation(s)
- Paul S P Bischof
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Theda U P Bartolomaeus
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Ulrike Löber
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Christoph Bleidorn
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen, Germany.
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.
- Biologische Anstalt Helgoland, Alfred Wegener Institute, Helgoland, Germany.
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Wu-Woods NJ, Barlow JT, Trigodet F, Shaw DG, Romano AE, Jabri B, Eren AM, Ismagilov RF. Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples. Nat Methods 2023; 20:1672-1682. [PMID: 37828152 PMCID: PMC10885704 DOI: 10.1038/s41592-023-02025-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/27/2023] [Indexed: 10/14/2023]
Abstract
Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.
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Affiliation(s)
- Natalie J Wu-Woods
- Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Jacob T Barlow
- Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Dustin G Shaw
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Committee on Immunology, The University of Chicago, Chicago, IL, USA
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Anna E Romano
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Committee on Immunology, The University of Chicago, Chicago, IL, USA
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Alfred-Wegener-Institute for Marine and Polar Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Rustem F Ismagilov
- Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA.
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4
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Mangal U, Noh K, Lee S, Cha JK, Song JS, Cha JY, Lee KJ, Kim KM, Kwon JS, Choi SH. Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies? J Periodontal Res 2023; 58:381-391. [PMID: 36641544 DOI: 10.1111/jre.13098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Microbiome from a "healthy cohort" is used as a reference for comparison to cases and intervention. However, the studies with cohort-based clinical research have not sufficiently accounted for the multistability in oral microbial community. The screening is limited to phenotypic features with marked variations in microbial genomic markers. Herein, we aimed to assess the stability of the oral microbiome across time from an intervention-free "healthy" cohort. METHODS We obtained 33 supragingival samples of 11 healthy participants from the biobank. For each participant, we processed one sample as baseline (T0) and two samples spaced at 1-month (T1) and 3-month (T2) intervals for 16S ribosomal RNA gene sequencing analysis. RESULTS We observed that taxonomic profiling had a similar pattern of dominant genera, namely, Rothia, Prevotella, and Hemophilus, at all time points. Shannon diversity revealed a significant increase from T0 (p < .05). Bray Curtis dissimilarity was significant (R = -.02, p < .01) within the cohort at each time point. Community stability had negative correlation to synchrony (r = -.739; p = .009) and variance (r = -.605; p = .048) of the species. Clustering revealed marked differences in the grouping patterns between the three time points. For all time points, the clusters presented a substantially dissimilar set of differentially abundant taxonomic and functional biomarkers. CONCLUSION Our observations indicate towards the presence of multistable states within the oral microbiome in an intervention-free healthy cohort. For a conclusive and meaningful long-term reference, dental clinical research should account for multistability in the personalized therapy approach to improve the identification and classification of reliable markers.
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Affiliation(s)
- Utkarsh Mangal
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kowoon Noh
- Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea.,Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea.,BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Seeyoon Lee
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Kook Cha
- Department of Periodontology, Research Institute of Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, Korea
| | - Je Seon Song
- Department of Pediatric Dentistry, Yonsei University College of Dentistry, Seoul, Korea.,Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea
| | - Jung-Yul Cha
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kee-Joon Lee
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kwang-Mahn Kim
- Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Sung Kwon
- Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea.,BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Sung-Hwan Choi
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
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Alonzo-De la Rosa CM, Miard S, Taubert S, Picard F. Methods to extract and study the biological effects of murine gut microbiota using Caenorhabditis elegans as a screening host. PLoS One 2023; 18:e0281887. [PMID: 36821579 PMCID: PMC9949637 DOI: 10.1371/journal.pone.0281887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Gut microbiota has been established as a main regulator of health. However, how changes in gut microbiota are directly associated with physiological and cellular alterations has been difficult to tackle on a large-scale basis, notably because of the cost and labor-extensive resources required for rigorous experiments in mammals. In the present study, we used the nematode Caenorhabditis elegans as a model organism to elucidate microbiota-host interactions. We developed a method to extract gut microbiota (MCB) from murine feces, and tested its potential as food source for and its impact on C. elegans biology compared to the standard bacterial diet Escherichia coli OP50. Although less preferred than OP50, MCB was not avoided but had a lower energy density (triglycerides and glucose). Consistently, MCB-fed worms exhibited smaller body length and size, lower fertility, and lower fat content than OP50-fed worms, but had a longer mean lifespan, which resembles the effects of calorie restriction in mammals. However, these outcomes were altered when bacteria were inactivated, suggesting an important role of symbiosis of MCB beyond nutrient source. Taken together, our findings support the effectiveness of gut MCB processing to test its effects in C. elegans. More work comparing MCB of differently treated mice or humans is required to further validate relevance to mammals before large-scale screening assays.
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Affiliation(s)
- Claudia Miriam Alonzo-De la Rosa
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Faculty of Pharmacy, Université Laval, Quebec, Canada
| | - Stéphanie Miard
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | - Stefan Taubert
- British Columbia Children’s Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Frédéric Picard
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Faculty of Pharmacy, Université Laval, Quebec, Canada
- * E-mail:
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Conti A, Casagrande Pierantoni D, Robert V, Corte L, Cardinali G. MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis. Microbiol Spectr 2023; 11:e0105222. [PMID: 36519933 PMCID: PMC9927109 DOI: 10.1128/spectrum.01052-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.
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Affiliation(s)
- Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | - Vincent Robert
- Westerdjik Institute for Biodiversity, Utrecht, Netherlands
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
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7
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Alqaisi MHM, Ekka MM, Patel BC. Forensic evaluation of mitochondrial DNA heteroplasmy in Gujarat population, India. Ann Hum Biol 2022; 49:332-341. [PMID: 36343161 DOI: 10.1080/03014460.2022.2144447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Owing to its high copy number and its small size, mtDNA analysis is the most reliable choice when biological materials from crime scenes are degraded or have mixed STR profiles. AIM To examine the occurrence of heteroplasmy along with its frequency and pattern in both HV1 and HV2 regions of the mtDNA among unrelated individuals from India. SUBJECTS AND METHODS Mitochondrial DNA control region [hypervariable region one (HV1) and hypervariable region two (HV2)] were analysed in blood and buccal tissues of 104 unrelated individuals from the Indian state of Gujarat. RESULTS A high frequency of point heteroplasmy (PH) and length heteroplasmy (LH) was revealed. PH was detected in 7.69% of the population, with a higher frequency observed in blood than in buccal samples. However, there were no statistically significant differences in PH between the two tissues (Chi-square = 0.552, p ≥ 0.05). A total of six PH positions were detected: three at HV1, and another three at HV2. The studied population showed 46.15% LH in the HV1 and HV2 regions of both tissues. The LH positions observed in the Gujarat population were the same as those previously reported at HV1 np16184-16193 and HV2 np303-315. CONCLUSIONS Our findings suggest that differences in the pattern of heteroplasmy found in different tissues can complicate the forensic analysis, on the other hand, the probability of a match between the questioned and reference samples increases when the heteroplasmy is identical in both tissues. Variability of PH among persons and even within tissues recommends analysing multiple tissue samples before drawing a conclusion in forensic mtDNA analyses.
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Affiliation(s)
- Mohammed H M Alqaisi
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Molina Madhulika Ekka
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Bhargav C Patel
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
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Ruuskanen MO, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R, Lahti L. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol 2022; 24:3840-3860. [PMID: 35229437 PMCID: PMC9790573 DOI: 10.1111/1462-2920.15945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
Abstract
Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.
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Affiliation(s)
- Matti O. Ruuskanen
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| | - Deepti Vats
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Renuka Potbhare
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Ameeta RaviKumar
- Institute of Bioinformatics and BiotechnologySavitribai Phule Pune UniversityPuneIndia
| | - Eveliina Munukka
- Microbiome Biobank, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Richa Ashma
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Leo Lahti
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
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Mohamad N, Azizan NI, Mokhtar NFK, Mustafa S, Mohd Desa MN, Hashim AM. Future perspectives on aptamer for application in food authentication. Anal Biochem 2022; 656:114861. [PMID: 35985482 DOI: 10.1016/j.ab.2022.114861] [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: 02/23/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Food fraudulence and food contamination are major concerns, particularly among consumers with specific dietary, cultural, lifestyle, and religious requirements. Current food authentication methods have several drawbacks and limitations, necessitating the development of a simpler, more sensitive, and rapid detection approach for food screening analysis, such as an aptamer-based biosensor system. Although the use of aptamer is growing in various fields, aptamer applications for food authentication are still lacking. In this review, we discuss the limitations of existing food authentication technologies and describe the applications of aptamer in food analyses. We also project several potential targets or marker molecules to be targeted in the SELEX process. Finally, this review highlights the drawbacks of current aptamer technologies and outlines the potential route of aptamer selection and applications for successful food authentication. This review provides an overview of the use of aptamer in food research and its potential application as a molecular reporter for rapid detection in food authentication process. Developing databases to store all biochemical profiles of food and applying machine learning algorithms against the biochemical profiles are urged to accelerate the identification of more reliable biomarker molecules as aptamer targets for food authentication.
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Affiliation(s)
- Nornazliya Mohamad
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Inani Azizan
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Fadhilah Khairil Mokhtar
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shuhaimi Mustafa
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Nasir Mohd Desa
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Faculty of Medicine and Health Science, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B. The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The worldwide rapid declines in insect and plant abundance and diversity that have occurred in the past decades have gained public attention and demand for political actions to counteract these declines are growing. Rapid large-scale biomonitoring can aid in observing these changes and provide information for decisions for land management and species protection. Malaise traps have long been used for insect sampling and when insects are captured in these traps, they carry traces of plants they have visited on the body surface or as digested food material in the gut contents. Metabarcoding offers a promising method for identifying these plant traces, providing insight into the plants with which insects are directly interacting at a given time. To test the efficacy of DNA metabarcoding with these sample types, 79 samples from 21 sites across Germany were analysed with the ITS2 barcode. This study, to our knowledge, is the first examination of metabarcoding plant DNA traces from Malaise trap samples. Here, we report on the feasibility of sequencing these sample types, analysis of the resulting taxa, the usage of cultivated plants by insects near nature conservancy areas and the detection of rare and neophyte species. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. Metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen and is the only possible identification method for the other plant traces from Malaise traps and could provide a broad utility for future studies of plant-insect interactions.
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Rupert R, Rodrigues KF, Chong HLH, Yong WTL. Dataset of 16S ribosomal DNA sequences of bacteria isolated from marine red algae Kappaphycus alvarezii. Data Brief 2022; 40:107784. [PMID: 35028352 PMCID: PMC8741434 DOI: 10.1016/j.dib.2021.107784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/25/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022] Open
Abstract
The data provided in the article contains bacterial community profiles present on the surface of red algae (Kappaphycus alvarezii) isolated directly after collection and after 30 days of cultivation in a closed circulation system. The explants of Kappaphycus alvarezii were cultivated in a laboratory setting under controlled growth conditions for 30 days in order to determine bacteria that could adapt to controlled culture conditions. Amplification and sequencing of bacterial 16S rDNA amplicon were performed on bacterial isolates associated with the seedlings. The 16S rDNA gene sequences were analyzed, trimmed, and assembled into contigs using DNA Baser Sequence Assembler (V5) software. Taxonomic identification for the assembled sequences was achieved using the online BLAST (blastn) algorithm, and the construction of a phylogenetic tree was performed using the MEGA7 software. The data reveals a distinct set of microbial variations between day one and day 30. The phylogenetic tree depicts four major clusters, Vibrio, Pseudoalteromonas, Alteromonas, and Bacterioplanes resident on the surface of the K. alvarezii. Comparison between these two bacterial groups provides evidence of the persistent marine bacteria that adapt to the long-term culture in closed circulation systems. Raw data files are available at the GenBank, NCBI database under the accession number of MZ570560 to MZ570580.
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12
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Liber JA, Minier DH, Stouffer-Hopkins A, Van Wyk J, Longley R, Bonito G. Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. PeerJ 2022; 10:e12701. [PMID: 35127279 PMCID: PMC8801177 DOI: 10.7717/peerj.12701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023] Open
Abstract
Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.
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Affiliation(s)
- Julian A. Liber
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States,Department of Biology, Duke University, Durham, North Carolina, United States
| | - Douglas H. Minier
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States
| | - Anna Stouffer-Hopkins
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States
| | - Judson Van Wyk
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
| | - Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
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13
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Malacrinò A. Host species identity shapes the diversity and structure of insect microbiota. Mol Ecol 2021; 31:723-735. [PMID: 34837439 DOI: 10.1111/mec.16285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/04/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022]
Abstract
As for most of the life that inhabits our planet, microorganisms play an essential role in insect nutrition, reproduction, defence, and support their host in many other functions. More recently, we assisted to an exponential growth of studies describing the taxonomical composition of bacterial communities across insects' phylogeny. However, there is still an outstanding question that needs to be answered: Which factors contribute most to shape insects' microbiomes? This study tries to find an answer to this question by taking advantage of publicly available sequencing data and reanalysing over 4000 samples of insect-associated bacterial communities under a common framework. Results suggest that insect taxonomy has a wider impact on the structure and diversity of their associated microbial communities than the other factors considered (diet, sex, life stage, sample origin and treatment). However, when specifically testing for signatures of codiversification of insect species and their microbiota, analyses found weak support for this, suggesting that while insect species strongly drive the structure and diversity of insect microbiota, the diversification of those microbial communities did not follow their host's phylogeny. Furthermore, a parallel survey of the literature highlights several methodological limitations that need to be considered in the future research endeavours.
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Affiliation(s)
- Antonino Malacrinò
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Münster, Germany
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14
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Ahannach S, Delanghe L, Spacova I, Wittouck S, Van Beeck W, De Boeck I, Lebeer S. Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples. iScience 2021; 24:103306. [PMID: 34765924 PMCID: PMC8571498 DOI: 10.1016/j.isci.2021.103306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022] Open
Abstract
Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition. Lysis buffer keeps the microbial composition stable during various storage conditions Host DNA depletion introduces a larger bias toward Gram-negative taxa The HostZERO Microbial DNA kit performed best in human DNA depletion for metagenomics Body site-specific approach based on microbial composition is needed to minimize bias
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Affiliation(s)
- Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lize Delanghe
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wannes Van Beeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke De Boeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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15
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Poulsen CS, Kaas RS, Aarestrup FM, Pamp SJ. Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns. Microbiol Spectr 2021; 9:e0138721. [PMID: 34612701 DOI: 10.1101/2021.05.24.445395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, -80°C; freezer, -20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We provide recommendations for sample storage and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a data set that could also be used for benchmarking algorithms to identify and correct for unwanted batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing be published together with DNA sequencing data at the International Nucleotide Sequence Database Collaboration (ENA/EBI, NCBI, DDBJ) or other repositories.
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Affiliation(s)
- Casper Sahl Poulsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Rolf Sommer Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
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16
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Poulsen CS, Kaas RS, Aarestrup FM, Pamp SJ. Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns. Microbiol Spectr 2021; 9:e0138721. [PMID: 34612701 PMCID: PMC8510183 DOI: 10.1128/spectrum.01387-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/11/2022] Open
Abstract
Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, -80°C; freezer, -20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We provide recommendations for sample storage and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a data set that could also be used for benchmarking algorithms to identify and correct for unwanted batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing be published together with DNA sequencing data at the International Nucleotide Sequence Database Collaboration (ENA/EBI, NCBI, DDBJ) or other repositories.
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Affiliation(s)
- Casper Sahl Poulsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rolf Sommer Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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17
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Kazantseva J, Malv E, Kaleda A, Kallastu A, Meikas A. Optimisation of sample storage and DNA extraction for human gut microbiota studies. BMC Microbiol 2021; 21:158. [PMID: 34051731 PMCID: PMC8164492 DOI: 10.1186/s12866-021-02233-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02233-y.
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Affiliation(s)
- Jekaterina Kazantseva
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia.
| | - Esther Malv
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aleksei Kaleda
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aili Kallastu
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Anne Meikas
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
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18
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Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021; 1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
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Affiliation(s)
| | | | | | - Joel A Boyd
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | - Liang Fang
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | | | | | - Lutz Krause
- Microba Life Sciences, Brisbane, QLD, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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19
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Abstract
Ureteral stents are commonly used medical devices that harbor a unique and patient-specific microbial community. This protocol describes an optimized procedure for high-quality DNA extraction from both urine and ureteral stent samples for the purpose of downstream microbiota characterization by amplicon sequencing. Detailed instruction is provided for 16S rRNA gene V4 region sequencing with the Illumina platform, which enables accurate and reproducible microbiota profiling of low bacterial abundance urine and stent samples. For complete details on the use and execution of this protocol, please refer to Al et al. (2020). The urinary tract harbors low-abundance microbiota capable of influencing health Traditional sample preparation yields variable results vulnerable to contamination Protocol optimizes urological specimen processing for 16S rRNA amplicon sequencing The method ensures high-quality, reproducible urological microbiota data generation
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Affiliation(s)
- Kait F Al
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.,Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jeremy P Burton
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.,Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.,Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
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20
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Wegl G, Grabner N, Köstelbauer A, Klose V, Ghanbari M. Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies. Front Microbiol 2021; 12:627539. [PMID: 33708184 PMCID: PMC7940207 DOI: 10.3389/fmicb.2021.627539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/01/2021] [Indexed: 11/24/2022] Open
Abstract
Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts.
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21
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Chirumbolo S. Swabbing Thoroughly People for COVID-19 Positivity. Insights on the Main Bio-analytical and Microbiology Bias and Concerns. Curr Microbiol 2020; 77:3680-3684. [PMID: 32814994 PMCID: PMC7437638 DOI: 10.1007/s00284-020-02167-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/11/2020] [Indexed: 01/12/2023]
Abstract
Thorough swabbing is becoming an increasing approach to fight COVID-19 transmission, particularly among asymptomatic subjects, who are thought to represent the majority of potentially-contacting people. Particularly in the current management of COVID-19 emergency, the 3T approach, i.e., testing, tracing and treating, is felt as particularly crucial to fight COVID-19 pandemic. Aside from the time-consuming, cost expensive and the many burdensome issues associated with a thorough swabbing, adopting easy-to-make criteria such as "drive-thru-swab" may exacerbate the burden of critical biases and pre-analytical errors, which may impair the analytical reliability of these tests. This manuscript addresses some major points about.
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Affiliation(s)
- Salvatore Chirumbolo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
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22
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Bacterial mock communities as standards for reproducible cytometric microbiome analysis. Nat Protoc 2020; 15:2788-2812. [PMID: 32770154 DOI: 10.1038/s41596-020-0362-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/27/2020] [Indexed: 11/09/2022]
Abstract
Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.
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23
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Wasimuddin, Schlaeppi K, Ronchi F, Leib SL, Erb M, Ramette A. Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework. Mol Ecol Resour 2020; 20:1558-1571. [PMID: 32599660 PMCID: PMC7693082 DOI: 10.1111/1755-0998.13215] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022]
Abstract
The 'One Health' framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extraction kits and commonly recommended primer pairs targeting different hypervariable regions (V3-V4, V4, V5-V6, V5-V6-V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F-806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F-806R revealed that soil and root samples have the highest estimates of species richness, while lowest richness was observed in human faeces. Primer pair choice directly influenced the estimation of community changes within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.
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Affiliation(s)
- Wasimuddin
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Francesca Ronchi
- Department for Biomedical Research, University of Bern, Inselspital, Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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24
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Cheema AS, Stinson LF, Lai CT, Geddes DT, Payne MS. DNA extraction method influences human milk bacterial profiles. J Appl Microbiol 2020; 130:142-156. [PMID: 32654260 DOI: 10.1111/jam.14780] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022]
Abstract
AIMS To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM). METHODS AND RESULTS Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0·68 ng μl-1 ) and QM (mean = 0·55 ng μl-1 ). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM. CONCLUSIONS Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk. SIGNIFICANCE AND IMPACT OF THE STUDY Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.
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Affiliation(s)
- A S Cheema
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - L F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - C T Lai
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - D T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - M S Payne
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, WA, Australia
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25
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Lim MY, Park YS, Kim JH, Nam YD. Evaluation of fecal DNA extraction protocols for human gut microbiome studies. BMC Microbiol 2020; 20:212. [PMID: 32680572 PMCID: PMC7367376 DOI: 10.1186/s12866-020-01894-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND DNA extraction is an important factor influencing the microbiome profile in fecal samples. Considering that the QIAamp DNA Stool Mini Kit, one of the most commonly used DNA extraction kits, is no longer manufactured, this study aimed to investigate whether a new commercially available kit, the QIAamp PowerFecal Pro DNA Kit, yields comparable microbiome profiles with those previously obtained using the QIAamp DNA Stool Mini Kit. RESULTS We extracted DNA from fecal samples of 10 individuals using three protocols (protocol P of the QIAamp PowerFecal Pro DNA Kit, and protocols SB and S of the QIAamp DNA Stool Mini Kit with and without an additional bead-beating step, respectively) in triplicate. Ninety extracted DNA samples were subjected to 16S rRNA gene sequencing. DNA quality measured by 260/280 absorbance ratios was found to be optimal in protocol P. Additionally, the DNA quantity and microbiome diversity obtained using protocol P were significantly higher than those of protocol S, however, did not differ significantly from those of protocol SB. Based on the overall microbiome profiles, variations between protocol P and protocol SB or S were significantly less than between-individual variations. Furthermore, most genera were not differentially abundant in protocol P compared to the other protocols, and the number of differentially abundant genera, as well as the degree of fold-changes were smaller between protocols P and SB than between protocols P and S. CONCLUSIONS The QIAamp PowerFecal Pro DNA Kit exhibited microbiome analysis results that were comparable with those of the QIAamp DNA Stool Mini Kit with a bead-beating step. These results will prove useful for researchers investigating the gut microbiome in selecting an alternative protocol to the widely used but discontinued kit.
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Affiliation(s)
- Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea
| | - Yong-Soo Park
- Food Processing Support Team, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea
| | - Jung-Ha Kim
- Department of Family Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, 06973, Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea. .,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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26
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Manzoor SS, Doedens A, Burns MB. The promise and challenge of cancer microbiome research. Genome Biol 2020; 21:131. [PMID: 32487228 PMCID: PMC7265652 DOI: 10.1186/s13059-020-02037-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodologies, especially culture-independent approaches, have accelerated and driven this research. Recent work has shed light on the multifaceted role that the community of organisms in and on the human body plays in cancer onset, development, detection, treatment, and outcome. Much remains to be discovered, however, as methodological variation and functional testing of statistical correlations need to be addressed for the field to advance.
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Affiliation(s)
| | - Annemiek Doedens
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA.
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27
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Venturini AM, Nakamura FM, Gontijo JB, da França AG, Yoshiura CA, Mandro JA, Tsai SM. Robust DNA protocols for tropical soils. Heliyon 2020; 6:e03830. [PMID: 32426533 PMCID: PMC7226647 DOI: 10.1016/j.heliyon.2020.e03830] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 09/06/2019] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.
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Affiliation(s)
- Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Fernanda Mancini Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Júlia Brandão Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Aline Giovana da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Caio Augusto Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Jéssica Adriele Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
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28
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Molina NM, Sola-Leyva A, Saez-Lara MJ, Plaza-Diaz J, Tubić-Pavlović A, Romero B, Clavero A, Mozas-Moreno J, Fontes J, Altmäe S. New Opportunities for Endometrial Health by Modifying Uterine Microbial Composition: Present or Future? Biomolecules 2020; 10:E593. [PMID: 32290428 PMCID: PMC7226034 DOI: 10.3390/biom10040593] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 02/08/2023] Open
Abstract
Current knowledge suggests that the uterus harbours its own microbiota, where the microbes could influence the uterine functions in health and disease; however, the core uterine microbial composition and the host-microbial relationships remain to be fully elucidated. Different studies are indicating, based on next-generation sequencing techniques, that microbial dysbiosis could be associated with several gynaecological disorders, such as endometriosis, chronic endometritis, dysfunctional menstrual bleeding, endometrial cancer, and infertility. Treatments using antibiotics and probiotics and/or prebiotics for endometrial microbial dysbiosis are being applied. Nevertheless there is no unified protocol for assessing the endometrial dysbiosis and no optimal treatment protocol for the established dysbiosis. With this review we outline the microbes (mostly bacteria) identified in the endometrial microbiome studies, the current treatments offered for bacterial dysbiosis in the clinical setting, and the future possibilities such as pro- and prebiotics and microbial transplants for modifying uterine microbial composition.
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Affiliation(s)
- Nerea M. Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
| | - Maria Jose Saez-Lara
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- “José Mataix Verdú” Institute of Nutrition and Food Technology (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18100 Granada, Spain
| | - Julio Plaza-Diaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- “José Mataix Verdú” Institute of Nutrition and Food Technology (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18100 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18011 Granada, Spain
| | | | - Barbara Romero
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Ana Clavero
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Juan Mozas-Moreno
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER Epidemiología y Salud Pública-CIBERESP), 28029 Madrid, Spain
- Departament of Obstetrics and Gynecology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Juan Fontes
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Competence Centre on Health Technologies, 50410 Tartu, Estonia
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29
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Kidd SE, Chen SCA, Meyer W, Halliday CL. A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready? Front Microbiol 2020; 10:2903. [PMID: 31993022 PMCID: PMC6971168 DOI: 10.3389/fmicb.2019.02903] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
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Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
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30
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Lactation and menstruation shift the vaginal microbiota in captive rhesus monkeys to be more similar to the male urethral microbiota. Sci Rep 2019; 9:17399. [PMID: 31758047 PMCID: PMC6874612 DOI: 10.1038/s41598-019-53976-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023] Open
Abstract
The vaginal microbiota of nonhuman primates differs substantially from humans in terms of Lactobacillus abundance, overall taxonomic diversity, and vaginal pH. Given these differences, it remains unclear in what way the nonhuman primate genital microbiota protects against pathogens, in particular sexually transmitted infections. Considering the effect that microbiota variations can have on disease acquisition and outcome, we examined endogenous and exogenous factors that influence the urogenital microbiota of male and female captive rhesus monkeys. The male urethral (n = 37) and vaginal (n = 194) microbiota of 11 breeding groups were examined in a cross-sectional study. During lactation and menstruation, the vaginal microbiota becomes significantly more diverse and more similar to the microbes observed in the male urethra. Group association and cage-mate (sexual partners) relationships were additionally associated with significant differences in the urogenital microbiota. Our results demonstrate that microbiota considerations are necessary in order to make informed selection of nonhuman primates as translational animal models.
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31
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Altmäe S, Franasiak JM, Mändar R. The seminal microbiome in health and disease. Nat Rev Urol 2019; 16:703-721. [PMID: 31732723 DOI: 10.1038/s41585-019-0250-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2019] [Indexed: 12/19/2022]
Abstract
Owing to the fact that there are more microbial than human cells in our body and that humans contain more microbial than human genes, the microbiome has huge potential to influence human physiology, both in health and in disease. The use of next-generation sequencing technologies has helped to elucidate functional, quantitative and mechanistic aspects of the complex microorganism-host interactions that underlie human physiology and pathophysiology. The microbiome of semen is a field of increasing scientific interest, although this microbial niche is currently understudied compared with other areas of microbiome research. However, emerging evidence is beginning to indicate that the seminal microbiome has important implications for the reproductive health of men, the health of the couple and even the health of offspring, owing to transfer of microorganisms to the partner and offspring. As this field expands, further carefully designed and well-powered studies are required to unravel the true nature and role of the seminal microbiome.
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Affiliation(s)
- Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain. .,Competence Centre on Health Technologies, Tartu, Estonia. .,Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain.
| | | | - Reet Mändar
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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32
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Gogarten JF, Calvignac-Spencer S, Nunn CL, Ulrich M, Saiepour N, Nielsen HV, Deschner T, Fichtel C, Kappeler PM, Knauf S, Müller-Klein N, Ostner J, Robbins MM, Sangmaneedet S, Schülke O, Surbeck M, Wittig RM, Sliwa A, Strube C, Leendertz FH, Roos C, Noll A. Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny. Mol Ecol Resour 2019; 20:204-215. [PMID: 31600853 DOI: 10.1111/1755-0998.13101] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 11/28/2022]
Abstract
Despite their ubiquity, in most cases little is known about the impact of eukaryotic parasites on their mammalian hosts. Comparative approaches provide a powerful method to investigate the impact of parasites on host ecology and evolution, though two issues are critical for such efforts: controlling for variation in methods of identifying parasites and incorporating heterogeneity in sampling effort across host species. To address these issues, there is a need for standardized methods to catalogue eukaryotic parasite diversity across broad phylogenetic host ranges. We demonstrate the feasibility of a metabarcoding approach for describing parasite communities by analysing faecal samples from 11 nonhuman primate species representing divergent lineages of the primate phylogeny and the full range of sampling effort (i.e. from no parasites reported in the literature to the best-studied primates). We detected a number of parasite families and regardless of prior sampling effort, metabarcoding of only ten faecal samples identified parasite families previously undescribed in each host (x̅ = 8.5 new families per species). We found more overlap between parasite families detected with metabarcoding and published literature when more research effort-measured as the number of publications-had been conducted on the host species' parasites. More closely related primates and those from the same continent had more similar parasite communities, highlighting the biological relevance of sampling even a small number of hosts. Collectively, results demonstrate that metabarcoding methods are sensitive and powerful enough to standardize studies of eukaryotic parasite communities across host species, providing essential new tools for macroecological studies of parasitism.
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Affiliation(s)
- Jan F Gogarten
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany.,Viral Evolution, Robert Koch-Institute Berlin, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany.,Viral Evolution, Robert Koch-Institute Berlin, Berlin, Germany
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Markus Ulrich
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany
| | - Nasrin Saiepour
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Henrik Vedel Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Fichtel
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Goettingen, Germany.,Leibniz Science Campus Primate Cognition, Goettingen, Germany
| | - Peter M Kappeler
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Goettingen, Germany.,Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute for Zoology, Georg-August University, Goettingen, Germany
| | - Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Nadine Müller-Klein
- Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany
| | - Julia Ostner
- Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
| | - Martha M Robbins
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Somboon Sangmaneedet
- Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Oliver Schülke
- Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
| | - Martin Surbeck
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
| | | | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Fabian H Leendertz
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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33
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Hallmaier-Wacker LK, Lüert S, Gronow S, Spröer C, Overmann J, Buller N, Vaughan-Higgins RJ, Knauf S. A Metataxonomic Tool to Investigate the Diversity of Treponema. Front Microbiol 2019; 10:2094. [PMID: 31552004 PMCID: PMC6746968 DOI: 10.3389/fmicb.2019.02094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
The genus Treponema contains a number of human and animal pathogenic as well as symbiotic bacteria that are found in vastly different anatomical and environmental habitats. Our understanding of the species range, evolution, and biology of these important bacteria is still limited. To explore the diversity of treponemes, we established, validated, and tested a novel metataxonomic approach. As the informative nature of the hypervariable regions of the 16S rRNA gene differ, we first analyzed each variable region independently. Considering the in silico results obtained, we established and validated the sequencing of the V4-region of the 16S rRNA gene using known mixtures of Treponema species as well as a selected number of clinical samples. The metataxonomic approach was able to identify Treponema to a near-species level. We demonstrate that using a spirochete-specific enrichment, our method is applicable to complex microbial communities and large variety of biological samples. The metataxonomic approach described provides a useful method to unravel the full diversity and range of Treponema in various ecosystems.
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Affiliation(s)
- Luisa K Hallmaier-Wacker
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Simone Lüert
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Nicky Buller
- Animal Pathology - Bacteriology Laboratory, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Rebecca J Vaughan-Higgins
- Department of Conservation Medicine, College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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34
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Asangba AE, Donohue ME, Lamb A, Wright PC, Halajian A, Leigh SR, Stumpf RM. Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity. Am J Primatol 2019; 81:e23045. [PMID: 31471974 DOI: 10.1002/ajp.23045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 01/01/2023]
Abstract
The study of the primate microbiome is critical in understanding the role of the microbial community in the host organism. To be able to isolate the main factors responsible for the differences observed in microbiomes within and between individuals, confounding factors due to technical variations need to be removed. To determine whether alterations due to preservatives outweigh differences due to factors such as host population, host species, body site, and habitat, we tested three methods (no preservative, 96% ethanol, and RNAlater) for preserving wild chimpanzee (fecal), wild lemur (fecal), wild vervet monkey (rectal, oral, nasal, otic, vaginal, and penile), and captive vervet monkey (rectal) samples. All samples were stored below - 20°C (short term) at the end of the field day and then at - 80°C until DNA extraction. Using 16S rRNA gene sequencing, we show a significant preservative effect on microbiota composition and diversity. Samples stored in ethanol and RNAlater appear to be less different compared with samples not stored in any preservative (none). Our differential analysis revealed significantly higher amounts of Enterococcaceae and Family XI in no preservative samples, Prevotellaceae and Spirochaetaceae in ethanol and RNAlater preserved samples, Oligosphaeraceae in ethanol-preserved samples, and Defluviitaleaceae in RNAlater preserved samples. While these preservative effects on the microbiome are not large enough to remove or outweigh the differences arising from biological factors (e.g., host species, body site, and habitat differences) they may promote misleading interpretations if they have large enough effect sizes compared to the biological factors (e.g., host population).
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Affiliation(s)
- Abigail E Asangba
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Alicia Lamb
- Department of Bioscience and Biotechnology, Clarkson University, Potsdam, New York
| | - Patricia C Wright
- Centre ValBio, Ranomafana, Madagascar.,Institute for the Conservation of Tropical Environments, Stony Brook University, Stony Brook, New York.,Department of Anthropology, Stony Brook University, Stony Brook, New York
| | - Ali Halajian
- Department of Biodiversity, University of Limpopo, Sovenga, South Africa
| | - Steven R Leigh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Anthropology, University of Colorado-Boulder, Boulder, Colorado
| | - Rebecca M Stumpf
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Vargas-Pellicer P, Watrobska C, Knowles S, Schroeder J, Banks-Leite C. How should we store avian faecal samples for microbiota analyses? Comparing efficacy and cost-effectiveness. J Microbiol Methods 2019; 165:105689. [PMID: 31425715 DOI: 10.1016/j.mimet.2019.105689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/15/2019] [Accepted: 08/15/2019] [Indexed: 10/26/2022]
Abstract
Analyses of bacterial DNA in faecal samples are becoming ever more common, yet we still do not know much about bird microbiomes. These challenges partly lie in the unique chemical nature of their faeces, and in the choice of sample storage method, which affects DNA preservation and the resulting microbiome composition. However, there is little information available on how best to preserve avian faeces for microbial analyses. This study evaluates five widely used methods for preserving nucleic acids and inferring microbiota profiles, for their relative efficacy, cost, and practicality. We tested the five methods (in-situ bead-beating with a TerraLyzer instrument, silica-bead desiccation, ethanol, refrigeration and RNAlater buffer) on 50 fresh faecal samples collected from captive House sparrows (Passer domesticus). In line with other studies, we find that different storage methods lead to distinct bacterial profiles. Storage method had a large effect on community composition and the relative abundance of dominant phyla such as Firmicutes and Proteobacteria, with the most significant changes observed for refrigerated samples. Furthermore, differences in the abundance of aerobic or facultatively aerobic taxa, particularly in refrigerated samples and those stored in ethanol, puts limits on comparisons of bacterial communities across different storage methods. Finally, the methods that did not include in-situ bead-beating did not recover comparable levels of microbiota to the samples that were immediately processed and preserved using a TerraLyzer device. However, this method is also less practical and more expensive under field work circumstances. Our study is the most comprehensive analysis to date on how storage conditions affect subsequent molecular assays applied to avian faeces and provides guidance on cost and practicality of methods under field conditions.
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Affiliation(s)
- Paula Vargas-Pellicer
- Department of Life Sciences, Silwood Park Campus, Imperial College London, SL5 7PY, UK.
| | - Cecylia Watrobska
- Department of Life Sciences, Silwood Park Campus, Imperial College London, SL5 7PY, UK; School of Biological Sciences, Royal Holloway University of London, TW20 0EY, UK
| | - Sarah Knowles
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, Herfordshire AL9 7TA, UK; Department of Zoology, University of Oxford, OX1 3SZ, UK
| | - Julia Schroeder
- Department of Life Sciences, Silwood Park Campus, Imperial College London, SL5 7PY, UK
| | - Cristina Banks-Leite
- Department of Life Sciences, Silwood Park Campus, Imperial College London, SL5 7PY, UK
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Guégan M, Minard G, Tran FH, Tran Van V, Dubost A, Valiente Moro C. Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota. FEMS Microbiol Ecol 2019; 94:5101426. [PMID: 30239661 DOI: 10.1093/femsec/fiy188] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/14/2018] [Indexed: 12/25/2022] Open
Abstract
Recent studies have highlighted the potential role of microbiota in the biology of the Aedes albopictus mosquito vector. This species is highly anthropogenic and exhibits marked ecological plasticity, with a resulting high potential to colonize a wide range of habitats-including anthropized areas-under various climatic conditions. We put forward the hypothesis that climate and anthropogenic activities, such as the use of antibiotics in agriculture and human medicine, might affect the mosquito-associated bacterial community. We thus studied the additive impact of a temperature decrease and antibiotic ingestion on the temporal dynamics of Ae. albopictus survival and its associated bacterial communities. The results showed no effects of disturbances on mosquito survival. However, short-term temperature impacts on bacterial diversity were observed, while both the community structure and bacterial diversity were affected by early antibiotic ingestion. The genera Elizabethkingia, Chryseobacterium and Wolbachia, as well as an unclassified member of the Bacteroidales order were particularly affected. Antibiotics negatively impacted Elizabethkingia abundance, while Chryseobacterium was completely eliminated following both disturbances, to the benefit of Wolbachia and the unclassified Bacteroidales species. These results generated fresh insight into the effects of climate and anthropogenic activities such as the use of antibiotics on mosquito microbiota.
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Affiliation(s)
- Morgane Guégan
- Université de Lyon, Ecologie microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Guillaume Minard
- Université de Lyon, Ecologie microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Florence-Hélène Tran
- Université de Lyon, Ecologie microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Van Tran Van
- Université de Lyon, Ecologie microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, Ecologie microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Claire Valiente Moro
- Université de Lyon, Ecologie microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1, Villeurbanne, France
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Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma. Sci Rep 2019; 9:10393. [PMID: 31316085 PMCID: PMC6637124 DOI: 10.1038/s41598-019-46535-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023] Open
Abstract
Though rare, breast implant-associated anaplastic large cell lymphoma (BIA-ALCL), a CD30+ T-cell lymphoma associated with textured breast implants, has adversely impacted our perception of the safety of breast implants. Its etiology unknown, one hypothesis suggests an initiating inflammatory stimulus, possibly infectious, triggers BIA-ALCL. We analyzed microbiota of breast, skin, implant and capsule in BIA-ALCL patients (n = 7), and controls via culturing methods, 16S rRNA microbiome sequencing, and immunohistochemistry. Alpha and beta diversity metrics and relative abundance of Gram-negative bacteria were calculated, and phylogenetic trees constructed. Staphylococcus spp., the most commonly cultured microbes, were identified in both the BIA-ALCL and contralateral control breast. The diversity of bacterial microbiota did not differ significantly between BIA-ALCL and controls for any material analyzed. Further, there were no significant differences in the relative abundance of Gram-negative bacteria between BIA-ALCL and control specimens. Heat maps suggested substantial diversity in the composition of the bacterial microbiota of the skin, breast, implant and capsule between patients with no clear trend to distinguish BIA-ALCL from controls. While we identified no consistent differences between patients with BIA-ALCL-affected and contralateral control breasts, this study provides insights into the composition of the breast microbiota in this population.
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On Controls in Ancient Microbiome Studies, and Microbial Resilience in Ancient Samples. Genes (Basel) 2018; 9:genes9100471. [PMID: 30262781 PMCID: PMC6210261 DOI: 10.3390/genes9100471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 11/28/2022] Open
Abstract
In the following comment, we reply to Eisenhofer and Weyrich’s letter “Proper authentication of ancient DNA is still essential” responding to the article “Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies” by Santiago-Rodriguez et al. One of the concerns raised was the possibility that the patterns noted in the gut microbiome of pre-Inca/Inca and Italian nobility mummies were due to contamination of the blank control. When examining the blank controls and filtering the operational taxonomic units (OTUs) present in the blank controls, and further performing in-silico contamination analyses, we noticed very similar patterns as those previously reported. We also discuss controls in ancient microbiome studies, and aspects of microbial resilience in ancient samples.
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Hayakawa T, Sawada A, Tanabe AS, Fukuda S, Kishida T, Kurihara Y, Matsushima K, Liu J, Akomo-Okoue EF, Gravena W, Kashima M, Suzuki M, Kadowaki K, Suzumura T, Inoue E, Sugiura H, Hanya G, Agata K. Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island. Primates 2018; 59:423-436. [DOI: 10.1007/s10329-018-0671-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/15/2018] [Indexed: 02/07/2023]
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