1
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Mukhopadhyay B. A reminder-peptidoglycan cell walls indeed occur in the archaeal domain, specifically in the members of Methanobacteria and Methanopyri classes. Front Microbiol 2024; 15:1329047. [PMID: 38784805 PMCID: PMC11111885 DOI: 10.3389/fmicb.2024.1329047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024] Open
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2
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Fry M. The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2024; 46:16. [PMID: 38530473 PMCID: PMC10965645 DOI: 10.1007/s40656-024-00616-8] [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: 03/07/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Efron St., Bat Galim, POB 9649, Haifa, 31096, Israel.
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3
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Forsdyke DR. Speciation, natural selection, and networks: three historians versus theoretical population geneticists. Theory Biosci 2024; 143:1-26. [PMID: 38282046 DOI: 10.1007/s12064-024-00412-9] [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: 02/03/2023] [Accepted: 01/06/2024] [Indexed: 01/30/2024]
Abstract
In 1913, the geneticist William Bateson called for a halt in studies of genetic phenomena until evolutionary fundamentals had been sufficiently addressed at the molecular level. Nevertheless, in the 1960s, the theoretical population geneticists celebrated a "modern synthesis" of the teachings of Mendel and Darwin, with an exclusive role for natural selection in speciation. This was supported, albeit with minor reservations, by historians Mark Adams and William Provine, who taught it to generations of students. In subsequent decades, doubts were raised by molecular biologists and, despite the deep influence of various mentors, Adams and Provine noted serious anomalies and began to question traditional "just-so-stories." They were joined in challenging the genetic orthodoxy by a scientist-historian, Donald Forsdyke, who suggested that a "collective variation" postulated by Darwin's young research associate, George Romanes, and a mysterious "residue" postulated by Bateson, might relate to differences in short runs of DNA bases (oligonucleotides). The dispute between a small network of historians and a large network of geneticists can be understood in the context of national politics. Contrasts are drawn between democracies, where capturing the narrative makes reversal difficult, and dictatorships, where overthrow of a supportive dictator can result in rapid reversal.
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Affiliation(s)
- Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L3N6, Canada.
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4
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Novikova PV, Bhanu Busi S, Probst AJ, May P, Wilmes P. Functional prediction of proteins from the human gut archaeome. ISME COMMUNICATIONS 2024; 4:ycad014. [PMID: 38486809 PMCID: PMC10939349 DOI: 10.1093/ismeco/ycad014] [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: 12/12/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 03/17/2024]
Abstract
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.
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Affiliation(s)
- Polina V Novikova
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8 BB, United Kingdom
| | - Alexander J Probst
- Environmental Metagenomics, Department of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, for Environmental Microbiology and Biotechnology, University Duisburg-Essen, Duisburg 47057, Germany
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Paul Wilmes
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
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5
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Yuwen L, Li X, Wu L, Luo Y, Su S. Construction of a point-of-care electrochemical biosensor for Escherichia coli 16S rRNA analysis based on MoS 2 nanoprobes. Analyst 2023; 148:6292-6296. [PMID: 37975852 DOI: 10.1039/d3an01693e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Foodborne pathogens are harmful to human health because they can contaminate food and induce diseases. To efficiently distinguish and determine foodborne bacteria, an ultrasensitive point-of-care electrochemical biosensor was designed for 16S rRNA detection by coupling a signal amplification strategy with MoS2-based nanoprobes. Gold nanoparticles and thionine co-functionalized molybdenum disulfide (MoS2) nanocomposites (MoS2-Thi-AuNPs) were used to construct nanoprobes, which can efficiently monitor the detection process and amplify the detection signal. In the presence of Escherichia coli (E. coli) 16S rRNA, a classical sandwiched DNA structure was formed on the surface of a hierarchical flower-like gold nanostructure-decorated screen-printed carbon electrode (HFGN-SPCE), generating an obvious electrochemical signal from Thi. Under optimal conditions, this designed electrochemical biosensor showed a wide dynamic range (0-1.0 × 106 fM), low detection limit (2.8 fM), high selectivity and accepted stability for E. coli 16S rRNA detection in ideal buffers. Moreover, this biosensor can efficiently determine 16S rRNA in milk samples and 10 CFU mL-1 bacterial lysate. All experimental results suggested that this biosensor has a promising application in the detection of foodborne pathogens.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Xinyi Li
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Liquan Wu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yi Luo
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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6
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Petrone JR, Rios Glusberger P, George CD, Milletich PL, Ahrens AP, Roesch LFW, Triplett EW. RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing. Front Microbiol 2023; 14:1201064. [PMID: 37547696 PMCID: PMC10402275 DOI: 10.3389/fmicb.2023.1201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis. Sequencing the near-entire rrn operon of bacteria and archaea enables the use of the universally conserved operon holding evolutionary polymorphisms for taxonomic resolution. Here, a reproducible and validated pipeline was developed, RRN-operon Enabled Species-level Classification Using EMU (RESCUE), to facilitate the sequencing of bacterial rrn operons and to support import into phyloseq. Benchmarking RESCUE showed that fully processed reads are now parallel or exceed the quality of Sanger, with median quality scores of approximately Q20+, using the R10.4 and Guppy SUP basecalling. The pipeline was validated through two complex mock samples, the use of multiple sample types, with actual Illumina data, and across four databases. RESCUE sequencing is shown to drastically improve classification to the species level for most taxa and resolves erroneous taxa caused by using short reads such as Illumina.
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7
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Campbell CD, Gleeson M, Sulaiman I. The role of the respiratory microbiome in asthma. FRONTIERS IN ALLERGY 2023; 4:1120999. [PMID: 37324782 PMCID: PMC10262749 DOI: 10.3389/falgy.2023.1120999] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023] Open
Abstract
Asthma is a common airways disease and the human microbiome plays an increasingly recognised role in asthma pathogenesis. Furthermore, the respiratory microbiome varies with asthma phenotype, endotype and disease severity. Consequently, asthma therapies have a direct effect on the respiratory microbiome. Newer biological therapies have led to a significant paradigm shift in how we treat refractory Type 2 high asthma. While airway inflammation is the generally accepted mechanism of action of all asthma therapies, including both inhaled and systemic therapies, there is evidence to suggest that they may also alter the microbiome to create a more functionally balanced airway microenvironment while also influencing airway inflammation directly. This downregulated inflammatory cascade seen biochemically, and reflected in improved clinical outcomes, supports the hypothesis that biological therapies may in fact affect the microbiome-host immune system dynamic and thus represent a therapeutic target for exacerbations and disease control.
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Affiliation(s)
- Christina D. Campbell
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Margaret Gleeson
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Imran Sulaiman
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
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8
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Liu W, Du Q, Zhang H, Han D. The gut microbiome and obstructive sleep apnea syndrome in children. Sleep Med 2022; 100:462-471. [PMID: 36252415 DOI: 10.1016/j.sleep.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 01/11/2023]
Abstract
Obstructive sleep apnea syndrome (OSAS) in children has become a major public health problem that affects the physical and mental growth of children. OSAS can result in adverse outcomes during growth and development, inhibiting the normal development of the metabolic, cardiovascular, and immune systems. OSAS is characterized by partial or complete obstruction of the upper airway, and prolonged obstruction that causes intermittent hypoxia and sleep fragmentation in children. The human microbiota is a complex community that is in dynamic equilibrium in the human body. Intermittent hypoxia and sleep fragmentation induced by childhood OSAS alter the composition of the gut microbiome. At the same time, changes in the gut microbiome affect sleep patterns in children through immunomodulatory and metabolic mechanisms, and induce further comorbidities, such as obesity, hypertension, and cardiovascular disease. This article discusses recent progress in research into the mechanisms of OSAS-induced changes in the gut microbiota and its pathophysiology in children.
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Affiliation(s)
- Wenxin Liu
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China
| | - Qingqing Du
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China
| | - Hong Zhang
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China.
| | - Dingding Han
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China.
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9
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Birla P, Shaikh FY. De- "bug"-ing the microbiome in lung cancer. Cancer Metastasis Rev 2022; 41:335-346. [PMID: 35588337 DOI: 10.1007/s10555-022-10036-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/30/2022] [Indexed: 12/12/2022]
Abstract
The identification of microbes enriched in the healthy lung has led to the compelling discovery that microbes may contribute to lung cancer pathogenesis. Here, we review the recent literature showing microbial associations with lung cancer as well as the functional features that have been identified in human and murine studies. Most biomarker data remain limited due to variable findings. However, multiple studies have found that lung tumors or ipsilateral airway samples have decreased α diversity compared to normal tissue. Specific genera, such as Veillonella and Streptococcus, were also found in association with lung tumors using multiple sampling methodologies. These microbes, which are generally found in the upper respiratory track, are associated with an IL-17 signature in the lung, potentially resulting in a pro-tumorigenic environment. Studies detailing these immune mechanisms are limited, and further investigation is necessary to delineate how these bacteria, their metabolites, and potentially tumor-associated neoantigens modulate the immune response in cancer.
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Affiliation(s)
- Pakhi Birla
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street CRB1 Bldg, Suite 4M 441, Baltimore, MD, 21231, USA
| | - Fyza Y Shaikh
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street CRB1 Bldg, Suite 4M 441, Baltimore, MD, 21231, USA.
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10
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Jüttner M, Ferreira-Cerca S. Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis. Mol Biol Evol 2022; 39:msac054. [PMID: 35275997 PMCID: PMC8997704 DOI: 10.1093/molbev/msac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
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Affiliation(s)
- Michael Jüttner
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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11
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Campbell CD, Barnett C, Sulaiman I. A clinicians’ review of the respiratory microbiome. Breathe (Sheff) 2022; 18:210161. [PMID: 36338247 PMCID: PMC9584600 DOI: 10.1183/20734735.0161-2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
The respiratory microbiome and its impact in health and disease is now well characterised. With the development of next-generation sequencing and the use of other techniques such as metabolomics, the functional impact of microorganisms in different host environments can be elucidated. It is now clear that the respiratory microbiome plays an important role in respiratory disease. In some diseases, such as bronchiectasis, examination of the microbiome can even be used to identify patients at higher risk of poor outcomes. Furthermore, the microbiome can aid in phenotyping. Finally, development of multi-omic analysis has revealed interactions between the host and microbiome in some conditions. This review, although not exhaustive, aims to outline how the microbiome is investigated, the healthy respiratory microbiome and its role in respiratory disease. The respiratory microbiome encompasses bacterial, fungal and viral communities. In health, it is a dynamic structure and dysbiotic in disease. Dysbiosis can be related to disease severity and may be utilised to predict patients at clinical risk.https://bit.ly/3pNSgnA
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12
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Ferreira-Cerca S. The dark side of the ribosome life cycle. RNA Biol 2022; 19:1045-1049. [PMID: 36082947 PMCID: PMC9467602 DOI: 10.1080/15476286.2022.2121421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Thanks to genetics, biochemistry, and structural biology many features of the ribosome´s life cycles in models of bacteria, eukaryotes, and some organelles have been revealed to near-atomic details. Collectively, these studies have provided a very detailed understanding of what are now well-established prototypes for ribosome biogenesis and function as viewed from a 'classical' model organisms perspective. However, very important challenges remain ahead to explore the functional and structural diversity of both ribosome biogenesis and function across the biological diversity on earth. Particularly, the 'third domain of life', the archaea, and also many non-model bacterial and eukaryotic organisms have been comparatively neglected. Importantly, characterizing these additional biological systems will not only offer a yet untapped window to enlighten the evolution of ribosome biogenesis and function but will also help to unravel fundamental principles of molecular adaptation of these central cellular processes.
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Affiliation(s)
- Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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13
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Abstract
The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France.
- Institute for Integrative biology of the Cell. université Paris-Saclay, Gif sur Yvette, France.
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14
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Ferreira-Cerca S, La Teana A, Londei P. Editorial: Archaeal Ribosomes: Biogenesis, Structure and Function. Front Microbiol 2021; 12:800052. [PMID: 34950128 PMCID: PMC8691397 DOI: 10.3389/fmicb.2021.800052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Anna La Teana
- Department of Life and Environmental Science, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Paola Londei
- Department Molecular Medicine, Policlinico Umberto I°Viale Regina, University of Rome Sapienza, Rome, Italy
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15
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Haarkötter C, Saiz M, Gálvez X, Medina-Lozano MI, Álvarez JC, Lorente JA. Usefulness of Microbiome for Forensic Geolocation: A Review. Life (Basel) 2021; 11:life11121322. [PMID: 34947853 PMCID: PMC8707258 DOI: 10.3390/life11121322] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Forensic microbiomics is a promising tool for crime investigation. Geolocation, which connects an individual to a certain place or location by microbiota, has been fairly well studied in the literature, and several applications have been found. The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.
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16
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Balch WE, Ferry JG. The Wolfe cycle of carbon dioxide reduction to methane revisited and the Ralph Stoner Wolfe legacy at 100 years. Adv Microb Physiol 2021; 79:1-23. [PMID: 34836609 DOI: 10.1016/bs.ampbs.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Methanogens are a component of anaerobic microbial consortia decomposing biomass to CO2 and CH4 that is an essential link in the global carbon cycle. One of two major pathways of methanogenesis involves reduction of the methyl group of acetate to CH4 with electrons from oxidation of the carbonyl group while the other involves reduction of CO2 to CH4 with electrons from H2 or formate. Pioneering investigations of the CO2 reduction pathway by Ralph S. Wolfe in the 70s and 80s contributed findings impacting the broader fields of biochemistry and microbiology that directed discovery of the domain Archaea and expanded research on anaerobic microbes for decades that continues to the present. This review presents an historical overview of the CO2 reduction pathway (Wolfe cycle) with recent developments, and an account of Wolfe's larger and enduring impact on the broad field of biology 100 years after his birth.
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Affiliation(s)
- William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.
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17
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Wu YQ, Yu ZG, Tang RB, Han GS, Anh VV. An Information-Entropy Position-Weighted K-Mer Relative Measure for Whole Genome Phylogeny Reconstruction. Front Genet 2021; 12:766496. [PMID: 34745231 PMCID: PMC8568955 DOI: 10.3389/fgene.2021.766496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022] Open
Abstract
Alignment methods have faced disadvantages in sequence comparison and phylogeny reconstruction due to their high computational costs in handling time and space complexity. On the other hand, alignment-free methods incur low computational costs and have recently gained popularity in the field of bioinformatics. Here we propose a new alignment-free method for phylogenetic tree reconstruction based on whole genome sequences. A key component is a measure called information-entropy position-weighted k-mer relative measure (IEPWRMkmer), which combines the position-weighted measure of k-mers proposed by our group and the information entropy of frequency of k-mers. The Manhattan distance is used to calculate the pairwise distance between species. Finally, we use the Neighbor-Joining method to construct the phylogenetic tree. To evaluate the performance of this method, we perform phylogenetic analysis on two datasets used by other researchers. The results demonstrate that the IEPWRMkmer method is efficient and reliable. The source codes of our method are provided at https://github.com/ wuyaoqun37/IEPWRMkmer.
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Affiliation(s)
- Yao-Qun Wu
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan, China.,Provincial Key Laboratory of Informational Service for Rural Area of Southwestern Hunan, Shaoyang University, Shaoyang, China
| | - Zu-Guo Yu
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan, China
| | - Run-Bin Tang
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan, China
| | - Guo-Sheng Han
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan, China
| | - Vo V Anh
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia
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18
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DasGupta S, Nykiel K, Piccirilli JA. The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes. RNA (NEW YORK, N.Y.) 2021; 27:1017-1024. [PMID: 34131025 PMCID: PMC8370743 DOI: 10.1261/rna.078813.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the evolution of biocatalysis. Despite suggestions that functional RNAs collectively form an interconnected web of neutral networks, little evidence has emerged to demonstrate the existence of such intersecting networks in naturally occurring RNAs. Here we show that neutral networks of two naturally occurring, seemingly unrelated endonucleolytic ribozymes, the hammerhead (HH) and hairpin (HP), intersect. Sequences at the intersection of these networks exhibit catalytic functions corresponding to both ribozymes by potentially populating both catalytic folds and enable a smooth crossover between the two. Small and structurally simple endonucleolytic motifs like the HH ribozyme could, through mutational walks along their neutral networks, encounter novel catalytic phenotypes, and structurally flexible, bifunctional sequences at the intersection of these networks could have acted as nodes for evolutionary diversification in an RNA world. Considering the simplicity and small size of the HH ribozyme, we propose that this self-cleaving motif could have been a precursor to other more complex endonucleolytic ribozymes. More generally, our results suggest that RNAs that possess distinct sequences, structures, and catalytic functions, can potentially share evolutionary history through mutational connections in sequence space.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kamila Nykiel
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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19
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Londei P, Ferreira-Cerca S. Ribosome Biogenesis in Archaea. Front Microbiol 2021; 12:686977. [PMID: 34367089 PMCID: PMC8339473 DOI: 10.3389/fmicb.2021.686977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.
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Affiliation(s)
- Paola Londei
- Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Sébastien Ferreira-Cerca
- Biochemistry III - Regensburg Center for Biochemistry, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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20
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Hassouneh SAD, Loftus M, Yooseph S. Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function. Front Microbiol 2021; 12:673632. [PMID: 34349736 PMCID: PMC8326577 DOI: 10.3389/fmicb.2021.673632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease of the gastrointestinal tract that is often characterized by abdominal pain, rectal bleeding, inflammation, and weight loss. Many studies have posited that the gut microbiome may play an integral role in the onset and exacerbation of IBD. Here, we present a novel computational analysis of a previously published IBD dataset. This dataset consists of shotgun sequence data generated from fecal samples collected from individuals with IBD and an internal control group. Utilizing multiple external controls, together with appropriate techniques to handle the compositionality aspect of sequence data, our computational framework can identify and corroborate differences in the taxonomic profiles, bacterial association networks, and functional capacity within the IBD gut microbiome. Our analysis identified 42 bacterial species that are differentially abundant between IBD and every control group (one internal control and two external controls) with at least a twofold difference. Of the 42 species, 34 were significantly elevated in IBD, relative to every other control. These 34 species were still present in the control groups and appear to play important roles, according to network centrality and degree, in all bacterial association networks. Many of the species elevated in IBD have been implicated in modulating the immune response, mucin degradation, antibiotic resistance, and inflammation. We also identified elevated relative abundances of protein families related to signal transduction, sporulation and germination, and polysaccharide degradation as well as decreased relative abundance of protein families related to menaquinone and ubiquinone biosynthesis. Finally, we identified differences in functional capacities between IBD and healthy controls, and subsequently linked the changes in the functional capacity to previously published clinical research and to symptoms that commonly occur in IBD.
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Affiliation(s)
- Sayf Al-Deen Hassouneh
- Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States
| | - Mark Loftus
- Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States
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21
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Yen S, Johnson JS. Metagenomics: a path to understanding the gut microbiome. Mamm Genome 2021; 32:282-296. [PMID: 34259891 PMCID: PMC8295064 DOI: 10.1007/s00335-021-09889-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022]
Abstract
The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.
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Affiliation(s)
- Sandi Yen
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK
| | - Jethro S Johnson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK.
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22
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Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
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Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
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23
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Tavakoli P, Vollmer-Conna U, Hadzi-Pavlovic D, Grimm MC. A Review of Inflammatory Bowel Disease: A Model of Microbial, Immune and Neuropsychological Integration. Public Health Rev 2021; 42:1603990. [PMID: 34692176 PMCID: PMC8386758 DOI: 10.3389/phrs.2021.1603990] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
Objective: Inflammatory bowel diseases (IBDs) are complex chronic inflammatory disorders of the gastro-intestinal (GI) tract with uncertain etiology. IBDs comprise two idiopathic disorders: Crohn's disease (CD) and ulcerative colitis (UC). The aetiology, severity and progression of such disorders are still poorly understood but thought to be influenced by multiple factors (including genetic, environmental, immunological, physiological, psychological factors and gut microbiome) and their interactions. The overarching aim of this review is to evaluate the extent and nature of the interrelationship between these factors with the disease course. A broader conceptual and longitudinal framework of possible neuro-visceral integration, core microbiome analysis and immune modulation assessment may be useful in accurately documenting and characterizing the nature and temporal continuity of crosstalk between these factors and the role of their interaction (s) in IBD disease activity. Characterization of these interactions holds the promise of identifying novel diagnostic, interventions, and therapeutic strategies. Material and Methods: A search of published literature was conducted by exploring PubMed, EMBASE, MEDLINE, Medline Plus, CDSR library databases. Following search terms relating to key question were set for the search included: "Inflammatory bowel diseases," "gut microbiota," "psychological distress and IBD," "autonomic reactivity and IBD," "immune modulation," "chronic inflammation," "gut inflammation," "enteric nervous system," "gut nervous system," "Crohn's disease," "Ulcerative colitis", "depression and IBD", "anxiety and IBD", "quality of life in IBD patients," "relapse in IBDs," "remission in IBDs," "IBD disease activity," "brain-gut-axis," "microbial signature in IBD," "validated questionnaires in IBD," "IBD activity indices," "IBD aetiology," "IBDs and stress," "epidemiology of IBDs", "autonomic nervous system and gut inflammation", "IBD and environment," "genetics of IBDs," "pathways of immune response in IBDs," "sleep disturbances in IBD," "hypothalamic-pituitary-adrenal axis (HPA)," "sympatho-adrenal axis," "CNS and its control of gut function" "mucosal immune response," "commensal and pathogenic bacteria in the gut," "innate and adaptive immunity." Studies evaluating any possible associations between gut microbiome, psychological state, immune modulation, and autonomic function with IBDs were identified. Commonly cited published literatures with high quality research methodology/results and additional articles from bibliographies of recovered papers were examined and included where relevant. Results: Although there is a substantial literature identifying major contributing factors with IBD, there has been little attempt to integrate some factors over time and assess their interplay and relationship with IBD disease activity. Such contributing factors include genetic and environmental factors, gut microbiota composition and function, physiological factors, psychological state and gut immune response. Interdependences are evident across psychological and biological factors and IBD disease activity. Although from the available evidence, it is implausible that a single explanatory model could elucidate the interplay between such factors and the disease course as well as the sequence of the effect during the pathophysiology of IBD. Conclusion: Longitudinal monitoring of IBD patients and integrating data related to the contributing/risk factors including psychological state, physiological conditions, inflammatory/immune modulations, and microbiome composition/function, could help to explain how major factors associate and interrelate leading to exacerbation of symptoms and disease activity. Identifying the temporal trajectory of biological and psychosocial disturbances may also help to assess their effects and interdependence on individuals' disease status. Moreover, this allows greater insight into understanding the temporal progressions of subclinical events as potential ground for disease severity in IBD. Furthermore, understanding the interaction between these risk factors may help better interventions in controlling the disease, reducing the costs related to disease management, further implications for clinical practice and research approaches in addition to improving patients' mental health and quality of life.
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Affiliation(s)
- P. Tavakoli
- St George and Sutherland Clinical School, Sydney, NSW, Australia
| | - U. Vollmer-Conna
- School of Psychiatry, University of New South Wales, Sydney, Australia
| | - D. Hadzi-Pavlovic
- School of Psychiatry, University of New South Wales, Sydney, Australia
| | - M. C. Grimm
- St George and Sutherland Clinical School, Sydney, NSW, Australia
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24
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Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers SV, Oeffinger M, Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res 2021; 49:1662-1687. [PMID: 33434266 PMCID: PMC7897474 DOI: 10.1093/nar/gkaa1268] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
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Affiliation(s)
- Robert Knüppel
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Michael Kern
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Felix Grünberger
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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25
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Indoor Microbial Exposures and Chronic Lung Disease: From Microbial Toxins to the Microbiome. Clin Chest Med 2021; 41:777-796. [PMID: 33153695 DOI: 10.1016/j.ccm.2020.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Effects of environmental microbial exposures on human health have long been of interest. Microbes were historically assumed to be harmful, but data have suggested that microbial exposures can modulate the immune system. We focus on the effects of indoor environmental microbial exposure on chronic lung diseases. We found contradictory data in bacterial studies using endotoxin as a surrogate for bacterial exposure. Contradictory data also exist in studies of fungal exposure. Many factors may modulate the effect of environmental microbial exposures on lung health, including coexposures. Future studies need to clarify which method of assessing environmental microbial exposures is most relevant.
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26
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Loftus M, Hassouneh SAD, Yooseph S. Bacterial associations in the healthy human gut microbiome across populations. Sci Rep 2021; 11:2828. [PMID: 33531651 PMCID: PMC7854710 DOI: 10.1038/s41598-021-82449-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
In a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. The human gut microbiome is believed to play an integral role in host health and disease. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, totaling over 1.6 Tbp, generated from 606 fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified 202 signature bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were constructed with these signature species using an approach based on the graphical lasso. Network analysis revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Bacterial species that form network modules, and species that constitute hubs and bottlenecks, were also identified. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional or structural differences.
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Affiliation(s)
- Mark Loftus
- grid.170430.10000 0001 2159 2859Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, 32787 USA
| | - Sayf Al-Deen Hassouneh
- grid.170430.10000 0001 2159 2859Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, 32787 USA
| | - Shibu Yooseph
- grid.170430.10000 0001 2159 2859Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816-2993 USA
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27
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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28
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Qu D, Qiao DF, Klintschar M, Qu Z, Yue X. High-throughput 16S rDNA sequencing assisting in the detection of bacterial pathogen candidates: a fatal case of necrotizing fasciitis in a child. Int J Legal Med 2020; 135:399-407. [PMID: 32895762 DOI: 10.1007/s00414-020-02421-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022]
Abstract
Postmortem detection of pathogens in infectious deaths is quite important for diagnosing the cause of death and public health. However, it is difficult to detect possible bacterial pathogens in forensic practice using conventional methods like bacterial culture, especially in cases with putrefaction and antibiotic treatment. We report a fatal case caused by necrotizing fasciitis due to bacterial infection. An 8-year-old girl was found dead during sleep 4 days after a minor trauma to her left knee. The gross autopsy suggested that bacterial soft tissue infection might be the cause of death, and the microscopic examination confirmed the diagnosis. The slight putrefaction found at gross autopsy might interfere through postmortem bacterial translocation and reproduction with bacterial culture. High-throughput 16S rDNA sequencing was employed to identify possible pathogens. Bacterial DNA sequencing results suggested Streptococcus pyogenes and Staphylococcus, typical pathogens of necrotizing fasciitis in the tissue. 16S rDNA sequencing might thus be a useful tool for accurate detection of pathogens in forensic practice.
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Affiliation(s)
- Dong Qu
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.,Institute of Legal Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Dong-Fang Qiao
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Zhi Qu
- Institute for Epidemiology, Social Medicine and Health Systems Research, Hannover Medical School, 30625, Hannover, Germany
| | - Xia Yue
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
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29
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Martin-Loeches I, Dickson R, Torres A, Hanberger H, Lipman J, Antonelli M, de Pascale G, Bozza F, Vincent JL, Murthy S, Bauer M, Marshall J, Cilloniz C, Bos LD. The importance of airway and lung microbiome in the critically ill. Crit Care 2020; 24:537. [PMID: 32867808 PMCID: PMC7457224 DOI: 10.1186/s13054-020-03219-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022] Open
Abstract
During critical illness, there are a multitude of forces such as antibiotic use, mechanical ventilation, diet changes and inflammatory responses that could bring the microbiome out of balance. This so-called dysbiosis of the microbiome seems to be involved in immunological responses and may influence outcomes even in individuals who are not as vulnerable as a critically ill ICU population. It is therefore probable that dysbiosis of the microbiome is a consequence of critical illness and may, subsequently, shape an inadequate response to these circumstances.Bronchoscopic studies have revealed that the carina represents the densest site of bacterial DNA along healthy airways, with a tapering density with further bifurcations. This likely reflects the influence of micro-aspiration as the primary route of microbial immigration in healthy adults. Though bacterial DNA density grows extremely sparse at smaller airways, bacterial signal is still consistently detectable in bronchoalveolar lavage fluid, likely reflecting the fact that lavage via a wedged bronchoscope samples an enormous surface area of small airways and alveoli. The dogma of lung sterility also violated numerous observations that long predated culture-independent microbiology.The body's resident microbial consortia (gut and/or respiratory microbiota) affect normal host inflammatory and immune response mechanisms. Disruptions in these host-pathogen interactions have been associated with infection and altered innate immunity.In this narrative review, we will focus on the rationale and current evidence for a pathogenic role of the lung microbiome in the exacerbation of complications of critical illness, such as acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Ignacio Martin-Loeches
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St James Hospital, Dublin 8., Ireland
- Department of Respiratory Medicine, Hospital Clinic, IDIBAPS, CIBERes, Barcelona, Spain
- Trinity College, Dublin, Ireland
| | - Robert Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, USA
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI USA
| | - Antoni Torres
- Deparment of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - SGR 911- Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Håkan Hanberger
- Department of Infectious Diseases, Linköping University, Linköping, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jeffrey Lipman
- The University of Queensland, Brisbane, Australia
- Scientific Consultant, Nimes University Hospital, University of Montpellier, Nimes, France
| | - Massimo Antonelli
- Department of Anesthesiology, Intensive Care and Emergency Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gennaro de Pascale
- Department of Anesthesiology, Intensive Care and Emergency Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Fernando Bozza
- National Institute of Infectious Diseases Evandro Chagas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Jean Louis Vincent
- Department of Intensive Care, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Srinivas Murthy
- University of British Columbia, Vancouver, BC V6H 3V4 Canada
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - John Marshall
- The Keenan Research Centre for Biomedical Science, The Li Ka Shing Knowledge Institute, St Michael’s Hospital, University of Toronto, Toronto, Ontario Canada
| | - Catia Cilloniz
- Deparment of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - SGR 911- Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Lieuwe D. Bos
- Department of Respiratory Medicine, Infection and Immunity, Amsterdam University Medical Center, AMC, Amsterdam, The Netherlands
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Diversity, ecology and evolution of Archaea. Nat Microbiol 2020; 5:887-900. [PMID: 32367054 DOI: 10.1038/s41564-020-0715-z] [Citation(s) in RCA: 210] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/30/2020] [Indexed: 12/23/2022]
Abstract
Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.
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31
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Gotschlich EC, Colbert RA, Gill T. Methods in microbiome research: Past, present, and future. Best Pract Res Clin Rheumatol 2020; 33:101498. [PMID: 32340923 DOI: 10.1016/j.berh.2020.101498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human microbiome is impressively immense and participates in many aspects of our health and wellness, particularly involving the development and maintenance of a healthy immune system. Not only do our microbes teach the immune system to fight infection, they also teach immune tolerance and help maintain homeostasis. From this knowledge, we have learned that the loss of tolerance to microbiota in both innate and adaptive processes plays an important role in immune-mediated and autoimmune disease. In this chapter, we will be discussing about methods used to study the microbiome, both old and new methods, fundamental concepts that have taken hold within the field, and how these principles relate to rheumatology, including thoughts on how microbiome research may be focused in the next decade.
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Affiliation(s)
- Emily C Gotschlich
- NIH/NIAMS, Building 4 Room 228, 4 Memorial Drive, Bethesda, MD 20892, USA.
| | - Robert A Colbert
- Pediatric Translational Research Branch, 10 Center Drive, Bldg. 10, Rm 12N240E, Bethesda, MD 20892, USA.
| | - Tejpal Gill
- Oregon Health and Science University, 3215 SW Pavilion Loop, Lamfrom Biomedical Research Building 253E, Portland, OR 97239, USA.
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32
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Sun Y, Liu Y, Pan J, Wang F, Li M. Perspectives on Cultivation Strategies of Archaea. MICROBIAL ECOLOGY 2020; 79:770-784. [PMID: 31432245 DOI: 10.1007/s00248-019-01422-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.
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Affiliation(s)
- Yihua Sun
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
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33
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Ophthalmic Manifestation of Tsukamurella Species: A Case Series and First Report of Ocular Implant Infection After Enucleation. Cornea 2019; 38:1328-1331. [PMID: 31246677 DOI: 10.1097/ico.0000000000001997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Tsukamurella is an important and emerging organism that causes opportunistic human infection. We present the largest case series of Tsukamurella species-associated ophthalmic infections, with an emphasis on clinical spectrum, risk factors, treatment, and outcome. METHODS A case series of culture-positive Tsukamurella species in ocular microbiological specimens was identified retrospectively from 2005 to 2018. Tsukamurella species were identified by phenotypic, molecular, and genotypic methods. Diagnoses were clinical and were supplemented by microbiological findings. Treatment including antibiotic type, number of antibiotics, treatment duration, and clinical outcome was documented. RESULTS Eleven cases of culture-positive Tsukamurella ocular infection were identified. Of these 54.5% (6/11) of cases resulted in conjunctivitis, 18% (2/11) of cases resulted in keratitis, and 9% (1/11) of cases resulted in blepharitis. One case of canaliculitis and 1 case of postenucleation ocular implant-related infection were reported, which were both novel findings. The presence of ocular implant and preexisting ocular surface diseases such as exposure keratopathy and ectropion were thought to be predisposing factors. We have demonstrated that treatment of Tsukamurella ocular conjunctivitis, keratitis, and blepharitis was effective using a combination therapy of 2 antibiotics (fluoroquinolone, fusidic acid, or chloramphenicol). Canaliculitis and ocular implant infection required further addition of oral antibiotics (macrolide or doxycycline), canaliculotomy, and removal of the infected implant for satisfactory management. CONCLUSIONS Tsukamurella tyrosinosolvens and Tsukamurella pulmonis were found to be the predominant species that caused ocular infection. Ocular manifestation of Tsukamurella has a wider spectrum than that previously reported. A high-level of suspicion and a low threshold for microbiological sampling in cases with prolonged ocular surface infection are recommended to diagnose Tsukamurella infections.
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34
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Spencer SP, Fragiadakis GK, Sonnenburg JL. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity 2019; 51:225-239. [PMID: 31433970 DOI: 10.1016/j.immuni.2019.08.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant "map" of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this field's current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.
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Affiliation(s)
- Sean P Spencer
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA.
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35
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Song Y, Zhao H, Wang T. An adaptive independence test for microbiome community data. Biometrics 2019; 76:414-426. [DOI: 10.1111/biom.13154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 09/16/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Yaru Song
- Department of Bioinformatics and BiostatisticsShanghai Jiao Tong University Shanghai China
- SJTU‐Yale Joint Center for Biostatistics and Data ScienceShanghai Jiao Tong University Shanghai China
| | - Hongyu Zhao
- Department of BiostatisticsYale University New Haven Connecticut
- SJTU‐Yale Joint Center for Biostatistics and Data ScienceShanghai Jiao Tong University Shanghai China
| | - Tao Wang
- Department of Bioinformatics and BiostatisticsShanghai Jiao Tong University Shanghai China
- SJTU‐Yale Joint Center for Biostatistics and Data ScienceShanghai Jiao Tong University Shanghai China
- MoE Key Lab of Artificial IntelligenceShanghai Jiao Tong University Shanghai China
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36
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Abstract
Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Thomas A Richards
- Biosciences and Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003 Barcelona, Spain
| | - Stefano Pagliara
- Biosciences and Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TU, UK
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37
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Li X, Lau SKP, Woo PCY. Molecular characterisation of emerging pathogens of unexplained infectious disease syndromes. Expert Rev Mol Diagn 2019; 19:839-848. [PMID: 31385539 DOI: 10.1080/14737159.2019.1651200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: The discoveries of HIV and Helicobacter pylori in the 1980s were landmarks in identification of novel pathogens causing unexplained infectious syndromes using conventional microbiological technologies. In the last few decades, advancement of molecular technologies has provided us with more robust tools to expand our armamentarium in this microbial hunting process. Areas covered: In this article, we give a brief overview of the most important molecular technologies we use for identification of emerging microbes associated with unexplained infectious syndromes, including 16S rRNA and other conserved targets sequencing for bacteria, internal transcribed spacer (ITS) and other target gene sequencing for fungi, polymerase and other gene sequencing for viruses, as well as deep sequencing. Then, we use several representative examples to illustrate how these techniques have been used for the discoveries of a few notable bacterial, fungal and viral pathogens associated with unexplained infectious syndromes in the last 20-30 years. Expert opinion: In the past and present, characterization of emerging pathogens of unexplained infectious disease syndromes has relied on a combination of conventional culture- and phenotype-based technologies and nucleic acid amplification and sequencing. In the next era, we envisage more widespread adoption of next generation technologies that can detect both known and previously undescribed pathogens.
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Affiliation(s)
- Xin Li
- Department of Microbiology, The University of Hong Kong , Hong Kong , China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong , Hong Kong , China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong , China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong , China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University , Hangzhou , China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong , Hong Kong , China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong , China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong , China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University , Hangzhou , China
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38
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Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi JJ, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, James BT, Sun F, Morgenstern B, Karlowski WM. Benchmarking of alignment-free sequence comparison methods. Genome Biol 2019; 20:144. [PMID: 31345254 PMCID: PMC6659240 DOI: 10.1186/s13059-019-1755-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. RESULTS Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. CONCLUSION The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.
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Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Hani Z Girgis
- Tandy School of Computer Science, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK, 74104, USA
| | | | - Chris-Andre Leimeister
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Kujin Tang
- Department of Biological Sciences, Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Thomas Dencker
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Anna Katharina Lau
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Sophie Röhling
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Jae Jin Choi
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michael S Waterman
- Department of Biological Sciences, Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433, China
| | - Matteo Comin
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Sung-Hou Kim
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susana Vinga
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NIH/NCI), Bethesda, USA
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin T James
- Tandy School of Computer Science, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK, 74104, USA
| | - Fengzhu Sun
- Department of Biological Sciences, Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433, China
| | - Burkhard Morgenstern
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Wojciech M Karlowski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
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Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:310-319. [PMID: 30550857 PMCID: PMC6364046 DOI: 10.1016/j.gpb.2018.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 11/23/2022]
Abstract
We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
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40
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Methanogens: pushing the boundaries of biology. Emerg Top Life Sci 2018; 2:629-646. [PMID: 33525834 PMCID: PMC7289024 DOI: 10.1042/etls20180031] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/15/2023]
Abstract
Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for energy conservation by methanogens and identifies gaps in methanogen biology that may be filled by undiscovered or yet-to-be engineered organisms.
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41
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The molecular and phenotypic characterization of fructophilic lactic acid bacteria isolated from the guts of Apis mellifera L. derived from a Polish apiary. J Appl Genet 2018; 59:503-514. [DOI: 10.1007/s13353-018-0467-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
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42
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Abstract
Microbiomes can be thought of as the integration of biotic and abiotic factors, including the microbial communities and the distinct physio-chemical properties that are present in a habitat. The microbes within a microbiome can influence the chemical environment by degrading medications inside patients or contaminants in the environment, such as hydrocarbons released after the Deepwater Horizon oil spill. Identifying and monitoring the relative abundance of microbes can help to elucidate variations in their response to toxins and should be considered as a variable in statistical analyses. In addition, the presence of pathogenic microbes or toxin-producing species could affect the observed toxicity of an environment. The protocols in this unit begin with the collection of samples, proceeds to sequencing of the bacterial DNA, and ends with an analysis of the bacterial community in light of environmental metadata. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jacquelynn Benjamino
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Lidia Beka
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
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43
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Ren J, Bai X, Lu YY, Tang K, Wang Y, Reinert G, Sun F. Alignment-Free Sequence Analysis and Applications. Annu Rev Biomed Data Sci 2018; 1:93-114. [PMID: 31828235 PMCID: PMC6905628 DOI: 10.1146/annurev-biodatasci-080917-013431] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genome and metagenome comparisons based on large amounts of next generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads. Alignment-free approaches based on the counts of word patterns in NGS data do not depend on the complete genome and are generally computationally efficient. Thus, they contribute significantly to genome and metagenome comparison. Recently, novel statistical approaches have been developed for the comparison of both long and shotgun sequences. These approaches have been applied to many problems including the comparison of gene regulatory regions, genome sequences, metagenomes, binning contigs in metagenomic data, identification of virus-host interactions, and detection of horizontal gene transfers. We provide an updated review of these applications and other related developments of word-count based approaches for alignment-free sequence analysis.
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Affiliation(s)
- Jie Ren
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Xin Bai
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Yang Young Lu
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Kujin Tang
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Ying Wang
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Gesine Reinert
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China
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44
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Teng JLL, Tang Y, Wong SSY, Fong JYH, Zhao Z, Wong CP, Chen JHK, Ngan AHY, Wu AKL, Fung KSC, Que TL, Lau SKP, Woo PCY. MALDI-TOF MS for identification of Tsukamurella species: Tsukamurella tyrosinosolvens as the predominant species associated with ocular infections. Emerg Microbes Infect 2018; 7:80. [PMID: 29739926 PMCID: PMC5940693 DOI: 10.1038/s41426-018-0083-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022]
Abstract
Although Tsukamurella infections have been increasingly reported in Europe, Asia, America, and Africa, indicating that diseases caused by this group of bacteria are emerging in a global scale, species identification within this genus is difficult in most clinical microbiology laboratories. Recently, we showed that groEL gene sequencing is useful for identification of all existing Tsukamurella species. Nevertheless, PCR sequencing is still considered expensive, time-consuming, and technically demanding, and therefore is yet to be incorporated as a routine identification method in clinical laboratories. Using groEL gene sequencing as the reference method, 60 Tsukamurella isolates were identified as five different Tsukamurella species [T. tyrosinosolvens (n = 31), T. pulmonis (n = 25), T. hongkongensis (n = 2), T. strandjordii (n = 1), and T. sinensis (n = 1)]. The most common source of the patient isolates were the eye (n = 18), sputum (n = 6), and blood (n = 6). None of the 60 isolates were identified correctly to species level by MALDI-TOF MS with the original Bruker database V.6.0.0.0. Using the Bruker database extended with 15 type and reference strains which covered all the currently recognized 11 Tsukamurella species, 59 of the 60 isolates were correctly identified to the species level with score ≥2.0. MALDI-TOF MS should be useful for routine species identification of Tsukamurella in clinical microbiology laboratories after optimization of the database. T. tyrosinosolvens was the most common species observed in patients with Tsukamurella infections and the predominant species associated with ocular infections.
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Affiliation(s)
- Jade L L Teng
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Ying Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samson S Y Wong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Jordan Y H Fong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhe Zhao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chun-Pong Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jonathan H K Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Antonio H Y Ngan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alan K L Wu
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | - Kitty S C Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Tak-Lun Que
- Department of Pathology, Tuen Mun Hospital, Hong Kong, China
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
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Matsuda M, Hirose Y, Kanauchi M, Hatanaka S, Totsuka A. Purification and Characteristics of Tannase Produced by Lactic Acid Bacteria, Lactobacillus Plantarum H78. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2016-4298-01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mari Matsuda
- Department of Food Management, Miyagi University Sendai, Miyagi, 2-2-1 Hatatate, Taihaku-ku, 982-0215, Japan
| | - Yayoi Hirose
- Department of Food Management, Miyagi University Sendai, Miyagi, 2-2-1 Hatatate, Taihaku-ku, 982-0215, Japan
| | - Makoto Kanauchi
- Department of Food Management, Miyagi University Sendai, Miyagi, 2-2-1 Hatatate, Taihaku-ku, 982-0215, Japan
| | - Sakiko Hatanaka
- Industrial Technology Institute, Miyagi Prefecture Government, 2-2 Akedori, Izumi-ku, Sendai, Miyagi, 981-3206, Japan
| | - Akira Totsuka
- Institute of Sensory Science, 1-5-2 Honcho, Naka-ku, Yokohama, Kanagawa, 213-0005, Japan
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Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing. Sci Rep 2018; 8:2028. [PMID: 29391471 PMCID: PMC5794912 DOI: 10.1038/s41598-018-19501-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/27/2017] [Indexed: 11/08/2022] Open
Abstract
Targeted sequencing promises to bring next-generation sequencing (NGS) into routine clinical use for infectious disease diagnostics. In this context, upfront processing techniques, including pathogen signature enrichment, must amplify multiple targets of interest for NGS to be relevant when applied to patient samples with limited volumes. Here, we demonstrate an optimized molecular inversion probe (MIP) assay targeting multiple variable regions within the 16S ribosomal gene for the identification of biothreat and ESKAPE pathogens in a process that significantly reduces complexity, labor, and processing time. Probes targeting the Klebsiella pneumoniae carbapenemase (KPC) antibiotic resistance (AR) gene were also included to demonstrate the ability to concurrently identify etiologic agent and ascertain valuable secondary genetic information. Our assay captured gene sequences in 100% of mock clinical samples prepared from flagged positive blood culture bottles. Using a simplified processing and adjudication method for mapped sequencing reads, genus and species level concordance was 100% and 80%, respectively. In addition, sensitivity and specificity for KPC gene detection was 100%. Our MIP assay produced sequenceable amplicons for the identification of etiologic agents and the detection of AR genes directly from blood culture bottles in a simplified single tube assay.
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Abstract
The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics.
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Natvig DO, Jackson DA, Taylor JW. RANDOM-FRAGMENT HYBRIDIZATION ANALYSIS OF EVOLUTION IN THE GENUS NEUROSPORA: THE STATUS OF FOUR-SPORED STRAINS. Evolution 2017; 41:1003-1021. [PMID: 28563413 DOI: 10.1111/j.1558-5646.1987.tb05873.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/1986] [Accepted: 05/19/1987] [Indexed: 12/01/2022]
Abstract
A random-fragment hybridization method employing nuclear DNA has been developed to explore phylogenetic relationships in the genus Neurospora. Four cloned fragments and repetitive rDNA sequences were examined for restriction-fragment polymorphisms among 14 strains representing four species. The findings demonstrate that variation among randomly selected nuclear fragments can be employed to group related taxa with a higher degree of resolution than has been obtained with other DNA hybridization methods, isozyme electrophoresis, or restriction analysis of repetitive DNA. Based on our analysis of cloned fragments, we conclude that four-spored, secondarily-homothallic strains collected worldwide represent a monophyletic group. Trees constructed on the basis of restriction-fragment cataloging and coarse-structure restriction-site maps are for the most part consistent with the present mating-based species concept. We are encouraged that this method will provide an additional important experimental tool for evolutionary studies.
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Affiliation(s)
- Donald O Natvig
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131
| | - David A Jackson
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131
| | - John W Taylor
- Department of Botany, University of California, Berkeley, CA, 94720
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A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies. Sci Data 2017; 4:170054. [PMID: 28440791 PMCID: PMC5404626 DOI: 10.1038/sdata.2017.54] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 03/20/2017] [Indexed: 11/13/2022] Open
Abstract
The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.
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