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Article ; Online: Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli

Michelle Qiu Carter / Bin Hu / Patrick S.G. Chain

Data in Brief, Vol 36, Iss , Pp 107065- (2021)

Transcriptomic data

2021

Abstract: Shiga toxin-producing Escherichia coli (STEC) strain RM13514 is a clinical isolate linked to the 2010 romaine lettuce-associated outbreak in the U.S. The genes encoding a type II restriction and modification system, PstI R-M, are located in a prophage ... ...

Abstract	Shiga toxin-producing Escherichia coli (STEC) strain RM13514 is a clinical isolate linked to the 2010 romaine lettuce-associated outbreak in the U.S. The genes encoding a type II restriction and modification system, PstI R-M, are located in a prophage genome that is also encoding Shiga toxin. In-frame deletion of the PstI R-M genes or dam, encoding a DNA adenine methylase, in strain RM13514 were generated, resulting in two mutant strains MQC599 and MQC602, respectively. The mutant strain MQC599 exhibited a similar growth rate as the wild-type (WT) strain RM13514 when grown in Luria-Bertani (LB) broth at 37 °C. In contrast, the growth of mutant strain MQC602 was significantly slower than either RM13514 or MQC599. Genes transcriptionally regulated by the PstI R-M system or by Dam were examined by the RNA-Seq based comparative transcriptomics. The total RNA was extracted from cells of each strain grown in LB broth at exponential and stationary phases. Three biological replicates were collected for each strain. After removal of ribosomal RNA, the mRNAs were converted to cDNAs followed by Illumina sequence library construction. For strains RM13514 and MQC599, six libraires were generated for each, three from the cells in the exponential growth phase and three from the cells in the stationary phase. For strain MQC602, three additional libraries were constructed from the cells in the early exponential growth phase. The resulting 21 libraries were combined in equal amounts and sequenced on an Illumina HighSeq 2000 instrument with the Paired End 100 bp (PE100) read format, generating a total of 45.83 Gbp sequence reads. This set of sequence data is available in the NCBI SRA database under the BioProject accession number PRJNA684587. This set of transcriptomic data provides information on methylation-mediated epigenetic regulation in STEC, an important foodborne pathogen that is frequently associated with large epidemic outbreaks and can cause life-threatening disease in humans [1]. This set of data will be useful for ...
Keywords	Shiga toxin-producing Escherichia coli (STEC) ; DNA adenine methylase (Dam) ; Restriction and modification (R-M) systems ; Epigenetic regulation ; RNA-Seq transcriptomics ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	612
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

Michelle Qiu Carter / Nicole Laniohan / Chien-Chi Lo / Patrick S. G. Chain

Microorganisms, Vol 10, Iss 866, p

2022 Volume 866

Abstract: Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to ... ...

Abstract	Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.
Keywords	Shiga toxin-producing Escherichia coli (STEC) ; pangenome ; pathogenicity islands ; virulence genes ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Gut Microbiome and Alcoholic Liver Disease

Erick S. LeBrun / Meghali Nighot / Viszwapriya Dharmaprakash / Anand Kumar / Chien-Chi Lo / Patrick S. G. Chain / Thomas Y. Ma

Life, Vol 11, Iss 7, p

Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice

2021 Volume 7

Abstract: Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and ... ...

Abstract	Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and phenotypes to specific members of gut microbiome communities. Here we utilized a chronic plus binge ethanol feed model (Gao-binge model) to explore microbiome community changes across three independent experiments performed in mice. We found significant and reproducible differences in microbiome community assemblies between ethanol-treated mice and control mice on the same diet absent of ethanol. We also identified significant differences in gut microbiota occurring temporally with ethanol treatment. Peak shift in communities was observed 4 days after the start of daily alcohol consumption. We quantitatively identified many of the bacterial genera indicative of these ethanol-induced shifts including 20 significant genera when comparing ethanol treatments with controls and 14 significant genera based on temporal investigation. Including overlap of treatment with temporal shifts, we identified 25 specific genera of interest in ethanol treatment microbiome shifts. Shifts coincide with observed presentation of fatty deposits in the liver tissue, i.e., Alcoholic Liver Disease-associated phenotype. The evidence presented herein, derived from three independent experiments, points to the existence of a common, reproducible, and characterizable “mouse ethanol gut microbiome”.
Keywords	gut microbiome ; microbial ecology ; indicator species ; bacterial communities ; mouse model ; alcohol effects ; Science ; Q
Subject code	590
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

Reid Longley / Aaron Robinson / Julian A. Liber / Abigail E. Bryson / Demosthenes P. Morales / Kurt LaButti / Robert Riley / Stephen J. Mondo / Alan Kuo / Yuko Yoshinaga / Chris Daum / Kerrie Barry / Igor V. Grigoriev / Alessandro Desirò / Patrick S. G. Chain / Gregory Bonito

Communications Biology, Vol 6, Iss 1, Pp 1-

2023 Volume 13

Abstract: Abstract Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and ... ...

Abstract	Abstract Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
Keywords	Biology (General) ; QH301-705.5
Subject code	590
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods.

Andrew W Bartlow / Zachary R Stromberg / Cheryl D Gleasner / Bin Hu / Karen W Davenport / Shailja Jakhar / Po-E Li / Molly Vosburg / Madhavi Garimella / Patrick S G Chain / Tracy H Erkkila / Jeanne M Fair / Harshini Mukundan

PLOS Global Public Health, Vol 2, Iss 7, p e

2022 Volume 0000811

Abstract: Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory ... ...

Abstract	Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.
Keywords	Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Building International Genomics Collaboration for Global Health Security

Helen H Cui / Tracy eErkkila / Patrick S G Chain / Momchilo eVuyisich

Frontiers in Public Health, Vol

2015 Volume 3

Abstract: Genome science and technologies are transforming life sciences globally in many ways, and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is ... ...

Abstract	Genome science and technologies are transforming life sciences globally in many ways, and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement and installation of next generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.
Keywords	Genomics ; bioinformatics ; Pathogen Detection ; global health ; One Health ; international collaboration ; Public aspects of medicine ; RA1-1270
Subject code	001
Language	English
Publishing date	2015-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recruiting human microbiome shotgun data to site-specific reference genomes.

Gary Xie / Chien-Chi Lo / Matthew Scholz / Patrick S G Chain

PLoS ONE, Vol 9, Iss 1, p e

2014 Volume 84963

Abstract: The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun ... ...

Abstract	The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago , Antarctica

Alison E. Murray / Nicole E. Avalon / Lucas Bishop / Karen W. Davenport / Erwan Delage / Armand E.K. Dichosa / Damien Eveillard / Mary L. Higham / Sofia Kokkaliari / Chien-Chi Lo / Christian S. Riesenfeld / Ryan M. Young / Patrick S.G. Chain / Bill J. Baker

Marine Drugs, Vol 18, Iss 298, p

2020 Volume 298

Abstract: Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study ...

Abstract	Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum , in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64° 46'S, 64° 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.
Keywords	Antarctica ; ascidian ; microbiome ; microbial diversity ; palmerolide A ; co-occurrence ; Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya.

PLoS Neglected Tropical Diseases, Vol 15, Iss 2, p e

2021 Volume 0008991

Abstract: Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread ... ...

Abstract	Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Subject code	580
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale

Bin Hu / Shane Canon / Emiley A. Eloe-Fadrosh / Anubhav / Michal Babinski / Yuri Corilo / Karen Davenport / William D. Duncan / Kjiersten Fagnan / Mark Flynn / Brian Foster / David Hays / Marcel Huntemann / Elais K. Player Jackson / Julia Kelliher / Po-E. Li / Chien-Chi Lo / Douglas Mans / Lee Ann McCue /

Nigel Mouncey / Christopher J. Mungall / Paul D. Piehowski / Samuel O. Purvine / Montana Smith / Neha Jacob Varghese / Donald Winston / Yan Xu / Patrick S. G. Chain

Frontiers in Bioinformatics, Vol

2022 Volume 1

Abstract: The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools ... ...

Abstract	The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.
Keywords	microbiome ; microbial ecology ; omics ; bioinformatics ; infrastructure ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	020
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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