1
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Wirdnam CD, Warmus D, Faso C. Nourseothricin as a novel drug for selection of transgenic Giardia lamblia. Int J Parasitol Drugs Drug Resist 2024; 25:100543. [PMID: 38685159 PMCID: PMC11067369 DOI: 10.1016/j.ijpddr.2024.100543] [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: 01/26/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Functional gene and protein characterizations in parasitic protists are often limited by their genetic tractability. Despite the development of CRISPR-Cas9-derived or inspired approaches for a handful of protist parasites, the overall genetic tractability of these organisms remains limited. The intestinal parasite Giardia lamblia is one such species, with the added challenge of a paucity of reliable selection markers. To address this limitation, we tested the feasibility of using Nourseothricin as an effective selection agent in Giardia. Here, we report that axenically-grown WB Giardia cells are sensitive to Nourseothricin and that engineering expression of the streptothricin acetyltransferase (SAT-1) gene from Streptomyces rochei in transgenic parasites confers resistance to this antibiotic. Furthermore, we determine that SAT-1-expressing parasites are cross-resistant neither to Neomycin nor Puromycin, which are widely used to select for transgenic parasites. Consequently, we show that Nourseothricin can be used in sequential combination with both Neomycin and Puromycin to select for dual transfection events. This work increases the number of reliable selection agents and markers for Giardia genetic manipulation, expanding the limited molecular toolbox for this species of global medical importance.
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Affiliation(s)
- Corina D Wirdnam
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3006 Bern, Switzerland
| | - Dawid Warmus
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3006 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Carmen Faso
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3006 Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Hallerstrasse 6, 3012 Bern, Switzerland; Institute for Infectious Diseases, University of Bern, Friedbuehlstrasse 25, 3001 Bern, Switzerland.
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2
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Spychała K, Piecuch A, Szleszkowski Ł, Kadej M, Ogórek R. Microscopic fungi on the corpse - Promising tool requiring further research. Forensic Sci Int 2024; 361:112129. [PMID: 38986228 DOI: 10.1016/j.forsciint.2024.112129] [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: 07/17/2023] [Revised: 01/21/2024] [Accepted: 06/29/2024] [Indexed: 07/12/2024]
Abstract
Forensic microbiology is a relatively new area of forensic sciences. It considers the potential of microorganisms to be used in criminal investigations. As most studies involve the role of bacteria in fields like post-mortem interval estimation, personal identification or geolocation, the data on the role of fungi is comparatively scarce. Forensic mycology involves the application of fungi and their structures in forensic cases. The aim of this review is the evaluation of the current state of knowledge on fungi associated with human cadavers and their possible role in estimating the time since death. In accordance with the available reports, we focused on the relation between microscopic fungi isolated from human corpses and the cadaver condition e.g., the stage of decomposition. We also emphasised the contrast between the reported methodologies and attempted to standardise research methods in forensic mycology from sample collection to its storage, mycological analysis and identification of the obtained fungal cultures. Moreover, the potential usage of microscopic fungi in criminal cases was discussed based on various case reports.
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Affiliation(s)
- Klaudyna Spychała
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
| | - Agata Piecuch
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
| | - Łukasz Szleszkowski
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 4, Wrocław PL-50-345, Poland
| | - Marcin Kadej
- Centre for Forensic Biology and Entomology, Department of Invertebrate Biology, Evolution and Conservation, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 65, Wrocław PL-51-148, Poland.
| | - Rafał Ogórek
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
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3
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Meng S, Peng T, Liu Y, Zhang S, Qian Z, Huang T, Xie Q, Gu JD, Hu Z. Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133907. [PMID: 38471380 DOI: 10.1016/j.jhazmat.2024.133907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/18/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
Abstract
Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Shan Zhang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Qingyi Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion -Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China; Offshore Environmental Pollution Control Engineering Research, Shantou University, Shantou, Guangdong 515063, PR China.
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Ovsepian A, Kardaras FS, Skoulakis A, Hatzigeorgiou AG. Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis. Front Microbiol 2024; 15:1383404. [PMID: 38659984 PMCID: PMC11041396 DOI: 10.3389/fmicb.2024.1383404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
The characterization of oral microbial communities and their functional potential has been shaped by metagenomics and metatranscriptomics studies. Here, a meta-analysis of four geographically and technically diverse oral shotgun metatranscriptomics studies of human periodontitis was performed. In total, 54 subgingival plaque samples, 27 healthy and 27 periodontitis, were analyzed. The core microbiota of the healthy and periodontitis group encompassed 40 and 80 species, respectively, with 38 species being common to both microbiota. The differential abundance analysis identified 23 genera and 26 species, that were more abundant in periodontitis. Our results not only validated previously reported genera and species associated with periodontitis with heightened statistical significance, but also elucidated additional genera and species that were overlooked in the individual studies. Functional analysis revealed a significant up-regulation in the transcription of 50 gene families (UniRef-90) associated with transmembrane transport and secretion, amino acid metabolism, surface protein and flagella synthesis, energy metabolism, and DNA supercoiling in periodontitis samples. Notably, the overwhelming majority of the identified gene families did not exhibit differential abundance when examined across individual datasets. Additionally, 4 bacterial virulence factor genes, including TonB dependent receptor from P. gingivalis, surface antigen BspA from T. forsynthia, and adhesin A (PsaA) and Type I glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the Streptococcus genus, were also found to be significantly more transcribed in periodontitis group. Microbial co-occurrence analysis demonstrated that the periodontitis microbial network was less dense compared to the healthy network, but it contained more positive correlations between the species. Furthermore, there were discernible disparities in the patterns of interconnections between the species in the two networks, denoting the rewiring of the whole microbial network during the transition to the disease state. In summary, our meta-analysis has provided robust insights into the oral active microbiome and transcriptome in both health and disease.
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Affiliation(s)
- Armen Ovsepian
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Filippos S. Kardaras
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Anargyros Skoulakis
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Artemis G. Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
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Fiore-Donno AM, Freudenthal J, Dahl MB, Rixen C, Urich T, Bonkowski M. Biotic interactions explain seasonal dynamics of the alpine soil microbiome. ISME COMMUNICATIONS 2024; 4:ycae028. [PMID: 38500704 PMCID: PMC10945362 DOI: 10.1093/ismeco/ycae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/24/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
While it is acknowledged that alpine soil bacterial communities are primarily driven by season and elevation, there is no consensus on the factors influencing fungi and protists. Here we used a holistic approach of the microbiome to investigate the seasonal dynamics in alpine grasslands, focusing on soil food web interactions. We collected 158 soil samples along elevation transects from three mountains in the Alps, in spring during snowmelt and in the following summer. Using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified into trophic guilds. Our findings reveal that the consumers' pressure increases from spring to summer, leading to more diverse and evenly distributed prey communities. Consequently, consumers effectively maintain the diverse soil bacterial and fungal communities essential for ecosystem functioning. Our research highlights the significance of biotic interactions in understanding the distribution and dynamics of alpine microbial communities.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Jule Freudenthal
- Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Mathilde Borg Dahl
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Christian Rixen
- WSL Institute for Snow and Avalanche Research SLF, 7260 Davos Dorf, Switzerland
- Climate Change, Extremes and Natural Hazards in Alpine Regions Research Centre CERC, 7260 Davos Dorf, Switzerland
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Michael Bonkowski
- Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
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6
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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7
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Salas-Espejo E, Terrón-Camero LC, Ruiz JL, Molina NM, Andrés-León E. Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms. Semin Reprod Med 2023; 41:125-143. [PMID: 38320576 DOI: 10.1055/s-0044-1779025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.
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Affiliation(s)
- Eduardo Salas-Espejo
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Laura C Terrón-Camero
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - José L Ruiz
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
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Sadeghi J, Hashemi Shahraki A, Chaganti SR, Heath D. Functional gene transcription variation in bacterial metatranscriptomes in large freshwater Lake Ecosystems: Implications for ecosystem and human health. ENVIRONMENTAL RESEARCH 2023; 231:116298. [PMID: 37268212 DOI: 10.1016/j.envres.2023.116298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023]
Abstract
Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three public beaches (Ontario, Canada) sampled in the winter (no ice), summer and fall (2019) showed relatively little spatial, but a strong temporal variation. Our data showed high transcriptional activity in summer and fall but surprisingly, 89% of the KEGG pathway genes and 60% of the selected candidate genes (52 genes) associated with physiological and ecological activity were still active in freezing temperatures (winter). Our data also supported the possibility of an adaptively flexible gene expression response of the freshwater BC to low temperature conditions (winter). Only 32% of the bacterial genera detected in the samples were active, indicating that the majority of detected taxa were non-active (dormant). We also identified high seasonal variation in the abundance and activity of taxa associated with health risks (i.e., Cyanobacteria and waterborne bacterial pathogens). This study provides a baseline for further characterization of freshwater BCs, health-related microbial activity/dormancy and the main drivers of their functional variation (such as rapid human-induced environmental change and climate change).
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | | | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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Hilderbrand RH, Bambakidis T, Crump BC. The Roles of Microbes in Stream Restorations. MICROBIAL ECOLOGY 2023; 85:853-861. [PMID: 36695828 DOI: 10.1007/s00248-023-02179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/18/2023] [Indexed: 05/04/2023]
Abstract
The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.
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Affiliation(s)
- Robert H Hilderbrand
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, USA.
| | - Ted Bambakidis
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
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