Approaches to querying bacterial genomes with transposon-insertion sequencing

Implementation of an adaptive laboratory evolution strategy for improved production of valuable microbial secondary metabolites

Microbial surface-active agents, such as rhamnolipids, represent an attractive substitute for synthetic surfactants. However, current production bioprocesses are generally inefficient. Adaptive laboratory evolution strategies could offer a promising avenue to improve secondary metabolites production. In the bacterium Burkholderia thailandensis, the social behaviour called swarming motility relies on biosynthesis of rhamnolipids. Since experimental swarming requires lower agar concentrations, we hypothesized that augmenting the agar concentration would constrain the cells to produce more rhamnolipids. Consecutive rounds of B. thailandensis cultivation on swarming media performed with increasing agar concentrations enhanced rhamnolipid production by the evolved populations, with a correlation between rhamnolipid production and agar concentrations. Whole-genome sequencing of superior producing evoluants revealed inactivating mutations in qsmR, which codes for a transcriptional regulator not known to influence rhamnolipid production. Results indicate that QsmR represses rhamnolipid biosynthetic genes transcription. The developed directed evolution strategy could be used to improve biosurfactant yields with other producing bacteria.

High-Throughput Tn-Seq Screens Identify Both Known and Novel Pseudomonas putida KT2440 Genes Involved in Metal Tolerance

Industrial and urban activities release toxic chemical waste into the environment. Pseudomonas putida, a soil bacterium, is known to degrade hydrocarbons and xenobiotics, and possesses numerous genes associated with heavy metal tolerance. Most studies on metal tolerance in P. putida focus solely on over- or underexpressed genes, potentially overlooking important genes with unchanged expression. This study employed a Tn-seq approach to identify the essential genes required for P. putida growth under metal stress. This method enables the identification of mutants with altered fitness in the presence of excess metals. The screen successfully identified a number of known genes implicated in metal resistance, including czcA-1, cadA-3, cadR, and pcoA2, thereby validating the approach. Further analyses using targeted mutagenesis and complementation assays revealed PP_5337 as a putative transcriptional regulator involved in copper tolerance and the two-component system RoxSR (PP_0887/PP_0888) as a key determinant of cadmium tolerance. Additionally, PP_1663 and PP_5002 were identified as contributing to cadmium and cobalt tolerance, respectively. This study provides the first evidence linking these genes to metal tolerance, highlighting gaps in our understanding of metal tolerance mechanisms in P. putida and demonstrating the utility of Tn-seq for identifying novel tolerance determinants.

Functional genomics of Campylobacter -host interactions in an intestinal tissue model reveals a small lipoprotein essential for flagellar assembly

Campylobacter jejuni is currently the most common cause of bacterial gastroenteritis worldwide. However, its genome provides few clues about how it interacts with the host. Moreover, infection screens have often been limited to classical cell culture or animal models. To identify C. jejuni genes involved in host cell interactions, we applied transposon sequencing in a humanized 3D intestinal infection model based on tissue engineering. This revealed key proteins required for host cell adherence and/or internalization, including an Rrf2 family transcriptional regulator as well as three so far uncharacterized genes ( pflC / Cj1643 , pflD / Cj0892c , pflE / Cj0978c ), which we demonstrate to encode factors essential for motility. Deletion mutants of pflC / D / E are non-motile but retain intact, paralysed flagella filaments. We demonstrate that two of these newly identified motility proteins, PflC and PflD, are components of the C. jejuni 's periplasmic disk structures of the high torque motor. The third gene, pflE , encodes a small protein of only 57 aa. Using CryoET imaging we uncovered that the small protein has a striking effect on motor biogenesis, leading to a complete loss of the flagellar disk and motor structures upon its deletion. While PflE does not appear to be a structural component of the motor itself, our data suggests that it is a lipoprotein and supports localization of the main basal disk protein FlgP, which is the first assembly step of the flagellar disk structure. Despite being annotated as a lipoprotein, we find that C. jejuni FlgP instead relies on PflE for its association with the outer membrane. Overall, our genome-wide screen revealed novel C. jejuni host interaction factors including a transcriptional regulator as well as two structural components and a small protein crucial for biogenesis of the C. jejuni high torque flagella motor. Since the flagella machinery is a critical virulence determining factor for C. jejuni , our work demonstrates how such a small protein can, quite literally, bring a bacterial pathogen to a halt.

The role of cydB gene in the biofilm formation by Campylobacter jejuni

Campylobacter jejuni is a major cause of food- and water-borne bacterial infections in humans. A key factor helping bacteria to survive adverse environmental conditions is biofilm formation ability. Nonetheless, the molecular basis underlying biofilm formation by C. jejuni remains poorly understood. Around thirty genes involved in the regulation and dynamics of C. jejuni biofilm formation have been described so far. We applied random transposon mutagenesis to identify new biofilm-associated genes in C. jejuni strain 81-176. Of 1350 mutants, twenty-four had a decreased ability to produce biofilm compared to the wild-type strain. Some mutants contained insertions in genes previously reported to affect the biofilm formation process. The majority of identified genes encoded hypothetical proteins. In the library of EZ-Tn5 insertion mutants, we found the cydB gene associated with respiration that was not previously linked with biofilm formation in Campylobacter. To study the involvement of the cydB gene in biofilm formation, we constructed a non-marked deletion cydB mutant together with a complemented mutant. We found that the cydB deletion-mutant formed a weaker biofilm of loosely organized structure and lower volume than the parent strain. In the present study, we demonstrated the role of the cydB gene in biofilm formation by C. jejuni.

Essential Genes Discovery in Microorganisms by Transposon-Directed Sequencing (Tn-Seq): Experimental Approaches, Major Goals, and Future Perspectives

Essential genes are crucial for microbial viability, playing key roles in both the primary and secondary metabolism. Since mutations in these genes can threaten organism viability, identifying them is challenging. Conditionally essential genes are required only under specific conditions and are important for functions such as virulence, immunity, stress survival, and antibiotic resistance. Transposon-directed sequencing (Tn-Seq) has emerged as a powerful method for identifying both essential and conditionally essential genes. In this review, we explored Tn-Seq workflows, focusing on eubacterial species and some yeast species. A comparison of 14 eubacteria species revealed 133 conserved essential genes, including those involved in cell division (e.g., ftsA, ftsZ), DNA replication (e.g., dnaA, dnaE), ribosomal function, cell wall synthesis (e.g., murB, murC), and amino acid synthesis (e.g., alaS, argS). Many other essential genes lack clear orthologues across different microorganisms, making them specific to each organism studied. Conditionally essential genes were identified in 18 bacterial species grown under various conditions, but their conservation was low, reflecting dependence on specific environments and microorganisms. Advances in Tn-Seq are expected to reveal more essential genes in the near future, deepening our understanding of microbial biology and enhancing our ability to manipulate microbial growth, as well as both the primary and secondary metabolism.

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the model organism Escherichia coli, as well as major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with the Keio E. coli single-gene deletion library often regarded as a gold standard. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of 13 sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first assess several gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations, we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently acquired essentiality multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival and identifies several instances of essential stress responses masked by redundancy in free-living bacteria.IMPORTANCEThe essential genome, that is the set of genes absolutely required to sustain life, is a core concept in genetics. Essential genes in bacteria serve as drug targets, put constraints on the engineering of biological chassis for technological or industrial purposes, and are key to constructing synthetic life. Despite decades of study, relatively little is known about how gene essentiality varies across related bacteria. In this study, we have collected gene essentiality data for 13 bacteria related to the model organism Escherichia coli, including several human pathogens, and investigated the conservation of essentiality. We find that approximately a third of the genes essential in any particular strain are non-essential in another related strain. Surprisingly, we do not find evidence for essential genes unique to specific genera; rather it appears a substantial fraction of the essential genome rapidly gains or loses essentiality during evolution. This suggests that essentiality is not an immutable characteristic but depends crucially on the genomic context. We illustrate this through a comparison of our essential genes in free-living bacteria to genes conserved in 34 insect endosymbionts with naturally reduced genomes, finding several cases where genes generally regarded as being important for specific stress responses appear to have become essential in endosymbionts due to a loss of functional redundancy in the genome.

Essential genes for Haemophilus parainfluenzae survival and biofilm growth

Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.

The role of cydB gene in the biofilm formation by Campylobacter jejuni

Campylobacter jejuni is a major cause of food- and water-borne bacterial infections in humans. A key factor helping bacteria to survive adverse environmental conditions is biofilm formation ability. Nonetheless, the molecular basis underlying biofilm formation by C. jejuni remains poorly understood. Around thirty genes involved in the regulation and dynamics of C. jejuni biofilm formation have been described so far. We applied random transposon mutagenesis to identify new biofilm-associated genes in C. jejuni strain 81-176. Of 1350 mutants, twenty-four had a decreased ability to produce biofilm compared to the wild-type strain. Some mutants contained insertions in genes previously reported to affect the biofilm formation process. The majority of identified genes encoded hypothetical proteins. In the library of EZ-Tn5 insertion mutants, we found the cydB gene associated with respiration that was not previously linked with biofilm formation in Campylobacter. To study the involvement of the cydB gene in biofilm formation, we constructed a non-marked deletion cydB mutant together with a complemented mutant. We found that the cydB deletion-mutant formed a weaker biofilm of loosely organized structure and lower volume than the parent strain. In the present study, we demonstrated the role of the cydB gene in biofilm formation by C. jejuni.

Gene essentiality in the solventogenic Clostridium acetobutylicum DSM 792

Clostridium acetobutylicum is a solventogenic, anaerobic, gram-positive bacterium that is commonly considered the model organism for studying acetone-butanol-ethanol fermentation. The need to produce these chemicals sustainably and with a minimal impact on the environment has revived the interest in research on this bacterium. The recent development of efficient genetic tools allows to better understand the physiology of this micro-organism, aiming at improving its fermentation capacities. Knowledge about gene essentiality would guide the future genetic editing strategies and support the understanding of crucial cellular functions in this bacterium. In this work, we applied a transposon insertion site sequencing method to generate large mutant libraries containing millions of independent mutants that allowed us to identify a core group of 418 essential genes needed for in vitro development. Future research on this significant biocatalyst will be guided by the data provided in this work, which will serve as a valuable resource for the community.

IMPORTANCE

Clostridium acetobutylicum is a leading candidate to synthesize valuable compounds like three and four carbons alcohols. Its ability to convert carbohydrates into a mixture of acetone, butanol, and ethanol as well as other chemicals of interest upon genetic engineering makes it an advantageous organism for the valorization of lignocellulose-derived sugar mixtures. Since, genetic optimization depends on the fundamental insights supplied by accurate gene function assignment, gene essentiality analysis is of great interest as it can shed light on the function of many genes whose functions are still to be confirmed. The data obtained in this study will be of great value for the research community aiming to develop C. acetobutylicum as a platform organism for the production of chemicals of interest.

Shedding light on bacteria-host interactions with the aid of TnSeq approaches

Bacteria are highly adaptable and grow in diverse niches, where they often interact with eukaryotic organisms. These interactions with different hosts span the entire spectrum from symbiosis to pathogenicity and thus determine the lifestyle of the bacterium. Knowledge of the genetic determinants involved in animal and plant host colonization by pathogenic and mutualistic bacteria is not only crucial to discover new drug targets for disease management but also for developing novel biostimulant strategies. In the last decades, significant progress in genome-wide high-throughput technologies such as transposon insertion sequencing has led to the identification of pathways that enable efficient host colonization. However, the extent to which similar genes play a role in this process in different bacteria is yet unclear. This review highlights the commonalities and specificities of bacterial determinants important for bacteria-host interaction.

Essential genes for Haemophilus parainfluenzae survival and biofilm growth

Haemophilus parainfluenzae ( Hp ) is a Gram-negative, pleomorphic rod, highly prevalent and abundant as a commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the tongue dorsum, keratinized gingiva, and the supragingival plaque biofilm. As a member of the HACEK group, Hp is also known to cause infective endocarditis. Additionally, case reports have identified Hp as the causative agent of meningitis, septic arthritis, chronic osteomyelitis, septicemia, and a variety of other infectious diseases. Little is known about how Hp interacts with its neighbors in the healthy biofilm nor about its mechanisms of pathogenesis as an extraoral opportunistic pathogen. To address these unknowns, we identified the essential genomes of two Hp strains and the conditionally essential genes for their growth in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain ( Hp 392) and a commensal oral isolate EL1 ( Hp EL1), we show that the essential genome of Hp 392 and Hp EL1 is composed of 395 and 384 genes, respectively. The core essential genome, consisting of 341 essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains of Hp . Additionally, RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic biofilm survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo oral habitat. Further, the creation of this library presents a valuable tool for further investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.

ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs

Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.

Genome-wide identification of fitness-genes in aminoglycoside-resistant Escherichia coli during antibiotic stress

Resistance against aminoglycosides is widespread in bacteria. This study aimed to identify genes that are important for growth of E. coli during aminoglycoside exposure, since such genes may be targeted to re-sensitize resistant E. coli to treatment. We constructed three transposon mutant libraries each containing > 230.000 mutants in E. coli MG1655 strains harboring streptomycin (aph(3″)-Ib/aph(6)-Id), gentamicin (aac(3)-IV), or neomycin (aph(3″)-Ia) resistance gene(s). Transposon Directed Insertion-site Sequencing (TraDIS), a combination of transposon mutagenesis and high-throughput sequencing, identified 56 genes which were deemed important for growth during streptomycin, 39 during gentamicin and 32 during neomycin exposure. Most of these fitness-genes were membrane-located (n = 55) and involved in either cell division, ATP-synthesis or stress response in the streptomycin and gentamicin exposed libraries, and enterobacterial common antigen biosynthesis or magnesium sensing/transport in the neomycin exposed library. For validation, eight selected fitness-genes/gene-clusters were deleted (minCDE, hflCK, clsA and cpxR associated with streptomycin and gentamicin resistance, and phoPQ, wecA, lpp and pal associated with neomycin resistance), and all mutants were shown to be growth attenuated upon exposure to the corresponding antibiotics. In summary, we identified genes that are advantageous in aminoglycoside-resistant E. coli during antibiotic stress. In addition, we increased the understanding of how aminoglycoside-resistant E. coli respond to antibiotic exposure.

Development and implementation of a Type I-C CRISPR-based programmable repression system for Neisseria gonorrhoeae

Clustered regularly interspaced short palindromic repeats (CRISPR) are prokaryotic adaptive immune systems regularly utilized as DNA-editing tools. While Neisseria gonorrhoeae does not have an endogenous CRISPR, the commensal species Neisseria lactamica encodes a functional Type I-C CRISPR-Cas system. We have established an isopropyl β-d-1-thiogalactopyranoside added (IPTG)-inducible, CRISPR interference (CRISPRi) platform based on the N. lactamica Type I-C CRISPR missing the Cas3 nuclease to allow locus-specific transcriptional repression. As proof of principle, we targeted a non-phase-variable version of the opaD gene. We show that CRISPRi can downregulate opaD gene and protein expression, resulting in bacterial inability to stimulate neutrophil oxidative responses and to bind to an N-terminal fragment of CEACAM1. Importantly, we used CRISPRi to effectively knockdown all the transcripts of all 11 opa genes using a five-spacer CRISPR array, allowing control of the entire phase-variable opa family in strain FA1090. We also report that repression is reversible following IPTG removal. Finally, we showed that the Type I-C CRISPRi system can conditionally reduce the expression of two essential genes. This CRISPRi system will allow the interrogation of every Gc gene, essential and non-essential, to study physiology and pathogenesis and aid in antimicrobial development.IMPORTANCEClustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have proven instrumental in genetically manipulating many eukaryotic and prokaryotic organisms. Despite its usefulness, a CRISPR system had yet to be developed for use in Neisseria gonorrhoeae (Gc), a bacterium that is the main etiological agent of gonorrhea infection. Here, we developed a programmable and IPTG-inducible Type I-C CRISPR interference (CRISPRi) system derived from the commensal species Neisseria lactamica as a gene repression system in Gc. As opposed to generating genetic knockouts, the Type I-C CRISPRi system allows us to block transcription of specific genes without generating deletions in the DNA. We explored the properties of this system and found that a minimal spacer array is sufficient for gene repression while also facilitating efficient spacer reprogramming. Importantly, we also show that we can use CRISPRi to knockdown genes that are essential to Gc that cannot normally be knocked out under laboratory settings. Gc encodes ~800 essential genes, many of which have no predicted function. We predict that this Type I-C CRISPRi system can be used to help categorize gene functions and perhaps contribute to the development of novel therapeutics for gonorrhea.

Recent advances in the characterization of essential genes and development of a database of essential genes

Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.

Recent Advances and Techniques for Identifying Novel Antibacterial Targets

BACKGROUND

With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly.

METHODS

In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification.

RESULTS

Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well.

CONCLUSION

The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.

Genome-wide identification of genes critical for in vivo fitness of multi-drug resistant porcine extraintestinal pathogenic Escherichia coli by transposon-directed insertion site sequencing using a mouse infection model

Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen. Recently, ExPEC has been reported to be an emerging problem in pig farming. However, the mechanism of pathogenicity of porcine ExPEC remains to be revealed. In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. By using a mouse infection model, a transposon-directed insertion site sequencing (TraDIS) assay was performed to identify in vivo fitness factors. By comparing the Tn insertion frequencies between the input Tn library and the recovered library from different organs, 64 genes were identified to be involved in fitness during systemic infection. 15 genes were selected and individual gene deletion mutants were constructed. The in vivo fitness was evaluated by using a competitive infection assay. Among them, ΔfimG was significantly outcompeted by the WT strain in vivo and showed defective adhesion to host cells. rfa which was involved in lipopolysaccharide biosynthesis was shown to be critical for in vivo fitness which may have resulted from its role in the resistance to serum killing. In addition, several metabolic genes including fepB, sdhC, fepG, gltS, dcuA, ccmH, ddpD, narU, glpD, malM, and yabL and two regulatory genes metJ and baeS were shown as important determinants of in vivo fitness of porcine ExPEC. Collectively, this study performed a genome-wide screening for in vivo fitness factors which will be important for understanding the pathogenicity of porcine ExPEC.

Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis

Salmonella enterica Enteritidis is the second most common serovar associated with invasive non-typhoidal Salmonella (iNTS) disease in sub-Saharan Africa. Previously, genomic and phylogenetic characterization of S . enterica Enteritidis isolates from the human bloodstream led to the discovery of the Central/Eastern African clade (CEAC) and West African clade, which were distinct from the gastroenteritis-associated global epidemic clade (GEC). The African S . enterica Enteritidis clades have unique genetic signatures that include genomic degradation, novel prophage repertoires and multi-drug resistance, but the molecular basis for the enhanced propensity of African S . enterica Enteritidis to cause bloodstream infection is poorly understood. We used transposon insertion sequencing (TIS) to identify the genetic determinants of the GEC representative strain P125109 and the CEAC representative strain D7795 for growth in three in vitro conditions (LB or minimal NonSPI2 and InSPI2 growth media), and for survival and replication in RAW 264.7 murine macrophages. We identified 207 in vitro -required genes that were common to both S . enterica Enteritidis strains and also required by S . enterica Typhimurium, S . enterica Typhi and Escherichia coli , and 63 genes that were only required by individual S . enterica Enteritidis strains. Similar types of genes were required by both P125109 and D7795 for optimal growth in particular media. Screening the transposon libraries during macrophage infection identified 177 P125109 and 201 D7795 genes that contribute to bacterial survival and replication in mammalian cells. The majority of these genes have proven roles in Salmonella virulence. Our analysis uncovered candidate strain-specific macrophage fitness genes that could encode novel Salmonella virulence factors.

Challenges and opportunities of strain diversity in gut microbiome research

Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.

Construction of a Transposon Mutant Library in the Pathogen Agrobacterium tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization

Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease on a wide range of host species by transferring and integrating a part of its own DNA (T-DNA) into the plant genome. The genes responsible of the above-mentioned processes are well characterized. However, a large number of the mechanisms involved in exploitation and colonization of the galls (also named plant tumors) remain unknown. Due to recent development of "transposon-sequencing" (Tn-Seq) techniques, a high-throughput screening and identification of the different genes involved in such mechanisms is now possible. In this chapter, we describe the detailed methodology used to construct a transposon library in A. tumefaciens and to conduct a Tn-Seq approach to discover genes involved in plant tumor exploitation and colonization.

Genome-wide analysis of fitness factors in uropathogenic Escherichia coli in a pig urinary tract infection model

Uropathogenic Escherichia coli (UPEC) is the primary cause of urinary tract infections (UTIs) in animals and humans. We applied Transposon-Directed Insertion Site sequencing (TraDIS) to determine the fitness genes in two well-characterized UPEC strains, UTI89 and CFT073, in order to identify fitness factors during UTI in a pig model. This novel animal model better reflects the course of UTI in humans than the commonly used mouse model, and facilitates the differentiation between sessile and planktonic UPEC populations. A total of 854 and 483 genes in UTI89 and CFT073, respectively, were predicted to contribute to growth in pig urine, and 1257 and 764, were scored as required for colonization of the bladder. The combined list of fitness genes for growth in urine and cystitis contained 741 (UTI89) and 439 (CFT073) genes. The essential genes for growth on LB agar media supplemented with kanamycin and the fitness factors during growth in human urine were also analyzed in CFT073. A total of 457 essential genes were identified and the pool of fitness genes for growth in human urine included 215 genes. The gene rfaG, which is involved in lipopolysaccharide biosynthesis, was included in all the fitness-gene-lists and was further confirmed to be relevant for all the conditions tested regardless of the host and the strain. Thus, this gene may represent a promising target for the development of new therapeutic strategies against UTI UPEC-associated. Besides this important observation, the study revealed strain-specific differences in gene-essentiality as well as in the fitness-gene-repertoire for growth in human urine and UTI of the pig model, and it identified novel factors required for UPEC-induced UTIs.

Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library

The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus.

The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a commensal of wild-caught mice, in CAST/EiJ mice, which persistently and asymptomatically colonizes. Approximately 500 candidate host interaction genes were identified. A subset of these are homologs of N. meningitidis and N. gonorrhoeae genes known to modulate pathogen-host interactions in vitro. Many candidate genes have no known function, demonstrating how much remains to be learned about N. musculi niche maintenance. As many genes of unknown function are conserved in human adapted Neisseria, they provide a gateway for understanding Neisseria persistence mechanisms in general.

Gradients in gene essentiality reshape antibacterial research

Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.

Exploiting transposons in the study of Staphylococcus aureus pathogenesis and virulence

The opportunistic pathogen Staphylococcus aureus has an extremely complex relationship with humans. While the bacteria can exist as a commensal in many, it can cause a wide range of diseases and infections when turned pathogenic. Its presence is a determinant of chronicity and poor prognosis in numerous diseases, and its genomic plasticity causes S. aureus antimicrobial resistance to be one of the most dire contemporary medical problems to solve. Genetic manipulation of S. aureus has led to numerous findings that are vital in the fight against its pathogenesis. The utilisation of transposon mutant libraries for the systematic inspection of the S. aureus genome led to many landmark discoveries pertaining to the bacteria's pathogenicity, antimicrobial resistance acquisition, and virulence regulation. In this review, we describe mutant libraries, and their significant contributions, from various S. aureus strains created with commonly used transposons. The general workflow for the construction of libraries will be presented, along with a discussion of the challenges of undertaking the task of large-scale library construction. As the accessibility of transposon mutant library construction, screening, and analysis increases, this genetic tool could be further exploited in the study of the S. aureus genome.

“Omics” Technologies - What Have They Told Us About Uropathogenic Escherichia coli Fitness and Virulence During Urinary Tract Infection?

Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infection (UTI), a widespread infectious disease of great impact on human health. This is further emphasized by the rapidly increase in antimicrobial resistance in UPEC, which compromises UTI treatment. UPEC biology is highly complex since uropathogens must adopt extracellular and intracellular lifestyles and adapt to different niches in the host. In this context, the implementation of forefront ‘omics’ technologies has provided substantial insight into the understanding of UPEC pathogenesis, which has opened the doors for new therapeutics and prophylactics discovery programs. Thus, ‘omics’ technologies applied to studies of UPEC during UTI, or in models of UTI, have revealed extensive lists of factors that are important for the ability of UPEC to cause disease. The multitude of large ‘omics’ datasets that have been generated calls for scrutinized analysis of specific factors that may be of interest for further development of novel treatment strategies. In this review, we describe main UPEC determinants involved in UTI as estimated by ‘omics’ studies, and we compare prediction of factors across the different ‘omics’ technologies, with a focus on those that have been confirmed to be relevant under UTI-related conditions. We also discuss current challenges and future perspectives regarding analysis of data to provide an overview and better understanding of UPEC mechanisms involved in pathogenesis which should assist in the selection of target sites for future prophylaxis and treatment.

Analysis of Gene Essentiality from TnSeq Data Using Transit

TnSeq, or sequencing of transposon insertion libraries, has proven to be a valuable method for probing the functions of genes in a wide range of bacteria. TnSeq has found many applications for studying genes involved in core functions (such as cell division or metabolism), stress response, virulence, etc., as well as to identify potential drug targets. Two of the most commonly used transposons in practice are Himar1, which inserts randomly at TA dinucleotides, and Tn5, which can insert more broadly throughout the genome. These insertions cause putative gene function disruption, and clones with insertions in genes that cannot tolerate disruption (in a given condition) are eliminated from the population. Deep sequencing can be used to efficiently profile the surviving members, with insertions in genes that can be inferred to be non-essential. Data from TnSeq experiments (i.e. transposon insertion counts at specific genomic locations) is inherently noisy, making rigorous statistical analysis (e.g. quantifying significance) challenging. In this chapter, we describe Transit, a Python-based software package for analyzing TnSeq data that combines a variety of data processing tools, quality assessment methods, and analytical algorithms for identifying essential (or conditionally essential) genes.

Delving into defence: identifying the Pseudomonas protegens Pf-5 gene suite involved in defence against secreted products of fungal, oomycete and bacterial rhizosphere competitors

Competitive behaviours of plant growth promoting rhizobacteria (PGPR) are integral to their ability to colonize and persist on plant roots and outcompete phytopathogenic fungi, oomycetes and bacteria. PGPR engage in a range of antagonistic behaviours that have been studied in detail, such as the production and secretion of compounds inhibitory to other microbes. In contrast, their defensive activities that enable them to tolerate exposure to inhibitory compounds produced by their neighbours are less well understood. In this study, the genes involved in the Pseudomonas protegens Pf-5 response to metabolites from eight diverse rhizosphere competitor organisms, Fusarium oxysporum, Rhizoctonia solani, Gaeumannomyces graminis var. tritici, Pythium spinosum, Bacillus subtilis QST713, Pseudomonas sp. Q2-87, Streptomyces griseus and Streptomyces bikiniensis subspecies bikiniensi, were examined. Proximity induced excreted metabolite responses were confirmed for Pf-5 with all partner organisms through HPLC before culturing a dense Pf-5 transposon mutant library adjacent to each of these microbes. This was followed by transposon-directed insertion site sequencing (TraDIS), which identified genes that influence Pf-5 fitness during these competitive interactions. A set of 148 genes was identified that were associated with increased fitness during competition, including cell surface modification, electron transport, nucleotide metabolism, as well as regulatory genes. In addition, 51 genes were identified for which loss of function resulted in fitness gains during competition. These included genes involved in flagella biosynthesis and cell division. Considerable overlap was observed in the set of genes observed to provide a fitness benefit during competition with all eight test organisms, indicating commonalities in the competitive response to phylogenetically diverse micro-organisms and providing new insight into competitive processes likely to take place in the rhizosphere.

Is amplification bias consequential in transposon sequencing (TnSeq) assays? A case study with a Staphylococcus aureus TnSeq library subjected to PCR-based and amplification-free enrichment methods

As transposon sequencing (TnSeq) assays have become prolific in the microbiology field, it is of interest to scrutinize their potential drawbacks. TnSeq data consist of millions of nucleotide sequence reads that are generated by PCR amplification of transposon-genomic junctions. Reads mapping to the junctions are enumerated thus providing information on the number of transposon insertion mutations in each individual gene. Here we explore the possibility that PCR amplification of transposon insertions in a TnSeq library skews the results by introducing bias into the detection and/or enumeration of insertions. We compared the detection and frequency of mapped insertions when altering the number of PCR cycles, and when including a nested PCR, in the enrichment step. Additionally, we present nCATRAs - a novel, amplification-free TnSeq method where the insertions are enriched via CRISPR/Cas9-targeted transposon cleavage and subsequent Oxford Nanopore MinION sequencing. nCATRAs achieved 54 and 23% enrichment of the transposons and transposon-genomic junctions, respectively, over background genomic DNA. These PCR-based and PCR-free experiments demonstrate that, overall, PCR amplification does not significantly bias the results of TnSeq insofar as insertions in the majority of genes represented in our library were similarly detected regardless of PCR cycle number and whether or not PCR amplification was employed. However, the detection of a small subset of genes which had been previously described as essential is sensitive to the number of PCR cycles. We conclude that PCR-based enrichment of transposon insertions in a TnSeq assay is reliable, but researchers interested in profiling putative essential genes should carefully weigh the number of amplification cycles employed in their library preparation protocols. In addition, nCATRAs is comparable to traditional PCR-based methods (Kendall's correlation=0.896-0.897) although the latter remain superior owing to their accessibility and high sequencing depth.

Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells

The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers toxic effectors to kill competitors or subvert some of their key functions. Here, we use transposon directed insertion-site sequencing to identify T6SS toxins associated with the H1-T6SS, one of the three T6SS machines found in Pseudomonas aeruginosa. This approach identified several putative toxin-immunity pairs, including Tse8-Tsi8. Full characterization of this protein pair demonstrated that Tse8 is delivered by the VgrG1a spike complex into prey cells where it targets the transamidosome, a multiprotein complex involved in protein synthesis in bacteria that lack either one, or both, of the asparagine and glutamine transfer RNA synthases. Biochemical characterization of the interactions between Tse8 and the transamidosome components GatA, GatB and GatC suggests that the presence of Tse8 alters the fine-tuned stoichiometry of the transamidosome complex, and in vivo assays demonstrate that Tse8 limits the ability of prey cells to synthesize proteins. These data expand the range of cellular components targeted by the T6SS by identifying a T6SS toxin affecting protein synthesis and validate the use of a transposon directed insertion site sequencing-based global genomics approach to expand the repertoire of T6SS toxins in T6SS-encoding bacteria.

Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria

Synechococcus elongatus PCC 7942 is a model cyanobacterium for study of the circadian clock, photosynthesis, and bioproduction of chemicals, yet nearly 40% of its gene identities and functions remain unknown, in part due to limitations of the existing genetic toolkit. While classical techniques for the study of genes (e.g., deletion or mutagenesis) can yield valuable information about the absence of a gene and its associated protein, there are limits to these approaches, particularly in the study of essential genes. Herein, we developed a tool for inducible degradation of target proteins in S. elongatus by adapting a method using degron tags from the Mesoplasma florum transfer-mRNA (tmRNA) system. We observed that M. florum lon protease can rapidly degrade exogenous and native proteins tagged with the cognate sequence within hours of induction. We used this system to inducibly degrade the essential cell division factor, FtsZ, as well as shell protein components of the carboxysome. Our results have implications for carboxysome biogenesis and the rate of carboxysome turnover during cell growth. Lon protease control of proteins offers an alternative approach for the study of essential proteins and protein dynamics in cyanobacteria.

Probabilistic Identification of Bacterial Essential Genes via insertion density using TraDIS Data with Tn5 libraries

Motivation

Probabilistic Identification of bacterial essential genes using transposon-directed insertion-site sequencing (TraDIS) data based on Tn5 libraries has received relatively little attention in the literature; most methods are designed for mariner transposon insertions. Analysis of Tn5 transposon-based genomic data is challenging due to the high insertion density and genomic resolution. We present a novel probabilistic Bayesian approach for classifying bacterial essential genes using transposon insertion density derived from transposon insertion sequencing data. We implement a Markov chain Monte Carlo sampling procedure to estimate the posterior probability that any given gene is essential. We implement a Bayesian decision theory approach to selecting essential genes. We assess the effectiveness of our approach via analysis of both simulated data and three previously published Escherichia coli, Salmonella Typhimurium and Staphylococcus aureus datasets. These three bacteria have relatively well characterized essential genes which allows us to test our classification procedure using receiver operating characteristic curves and area under the curves. We compare the classification performance with that of Bio-Tradis, a standard tool for bacterial gene classification.

Results

Our method is able to classify genes in the three datasets with areas under the curves between 0.967 and 0.983. Our simulated synthetic datasets show that both the number of insertions and the extent to which insertions are tolerated in the distal regions of essential genes are both important in determining classification accuracy. Importantly our method gives the user the option of classifying essential genes based on the user-supplied costs of false discovery and false non-discovery.

Availability and implementation

An R package that implements the method presented in this paper is available for download from https://github.com/Kevin-walters/insdens.

Supplementary information

Supplementary data are available at Bioinformatics online.

Genetic variation and function: revealing potential factors associated with microbial phenotypes

Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.

Protocols for Tn-seq Analyses in the Group A Streptococcus

Transposon-sequencing (Tn-seq) has revolutionized forward-genetic analyses to study genotype-phenotype associations and interrogate bacterial cell physiology. The Tn-seq approach allows the en masse monitoring of highly complex mutant libraries, leveraging massive parallel DNA sequencing as a means to characterize the composition of these mutant pools on a genome-scale with unprecedented nucleotide-level high resolution. In this chapter, we present step-by-step protocols for Tn-seq analyses in the human pathogen Streptococcus pyogenes (Group A Streptococcus or GAS) using the mariner-based Krmit transposon. We detail how to generate highly complex Krmit mutant libraries in GAS and the en masse production of Krmit insertion tags for Illumina sequencing of the transposon-genome junctions for Tn-seq analyses. Most of the protocols presented here were developed and implemented using the S. pyogenes M1T1 serotype clinical isolate 5448, but they have been successfully applied to multiple GAS serotypes as well as other pathogenic Streptococci.

Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing

Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacterium that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used for this species. In this study, we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses, and transport were underrepresented. The majority of Pf-5 essential genes were part of the P. protegens core genome. Comparison of the essential gene set of Pf-5 with those of two plant-associated pseudomonads, P. simiae and P. syringae, and the well-studied opportunistic human pathogen P. aeruginosa PA14 showed that the four species share a large number of essential genes, but each species also had uniquely essential genes. Comparison of the Pf-5 in silico-predicted and in vitro-determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles may improve our understanding of the biological processes important for bacterial survival and growth.IMPORTANCE Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analyses of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of three other pseudomonads highlights how gene essentiality varies between closely related species.

DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools

Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.

A mini-Tn5-derived transposon with reportable and selectable markers enables rapid generation and screening of insertional mutants in Gram-negative bacteria

We re-engineered a classic tool for mutagenesis and gene expression studies in Gram-negative bacteria. Our modified Tn5-based transposon contains multiple features that allow rapid selection for mutants, direct quantification of gene expression and straightforward cloning of the inactivated gene. The promoter-less gfp-km cassette provides selection and reporter assay depending on the activity of the promoter upstream of the transposon insertion site. The cat gene facilitates positive antibiotic selection for mutants, while the narrow R6Kγ replication origin forces transposition in recipient strains lacking the pir gene and enables cloning of the transposon flanked with the disrupted gene from the chromosome. The suicide vector pCKD100, a plasmid that could be delivered into recipient cells through biparental mating or electroporation, harbours the modified transposon. We used the transposon to mutagenize Pectobacterium versatile KD100, Pseudumonas coronafaciens PC27R and Escherichia coli 35150N. The fluorescence intensities of mutants expressing high GFP could be quantified and detected qualitatively. Transformation efficiency from conjugation ranged from 1600 to 1900 CFU per ml. We sequenced the upstream flanking regions, identified the putative truncated genes and demonstrated the restoration of the GFP phenotype through marker exchange. The mini-Tn5 transposon was also utilized to construct mutant a library of P. versatile for forward genetic screens.

High-Throughput Functional Genomics for Energy Production

Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Additionally, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.

Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis

By analyzing successive lifestyle stages of a model Rhizobium-legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N₂-fixing bacteroids, and release from legume (pea) nodules. While only 27 genes are annotated as nif and fix in Rhizobium leguminosarum, we show 603 genetic regions (593 genes, 5 transfer RNAs, and 5 RNA features) are required for the competitive ability to nodulate pea and fix N₂ Of these, 146 are common to rhizosphere growth through to bacteroids. This large number of genes, defined as rhizosphere-progressive, highlights how critical successful competition in the rhizosphere is to subsequent infection and nodulation. As expected, there is also a large group (211) specific for nodule bacteria and bacteroid function. Nodule infection and bacteroid formation require genes for motility, cell envelope restructuring, nodulation signaling, N₂ fixation, and metabolic adaptation. Metabolic adaptation includes urea, erythritol and aldehyde metabolism, glycogen synthesis, dicarboxylate metabolism, and glutamine synthesis (GlnII). There are 17 separate lifestyle adaptations specific to rhizosphere growth and 23 to root colonization, distinct from infection and nodule formation. These results dramatically highlight the importance of competition at multiple stages of a Rhizobium-legume symbiosis.

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

Transposon sequencing (Tn-seq) is a powerful method that combines transposon mutagenesis and massive parallel sequencing to identify genes and pathways that contribute to bacterial fitness under a wide range of environmental conditions. Tn-seq applications are extensive and have not only enabled examination of genotype-phenotype relationships at an organism level but also at the population, community and systems levels. Gram-negative bacteria are highly associated with antimicrobial resistance phenotypes, which has increased incidents of antibiotic treatment failure. Antimicrobial resistance is defined as bacterial growth in the presence of otherwise lethal antibiotics. The "last-line" antimicrobial colistin is used to treat Gram-negative bacterial infections. However, several Gram-negative pathogens, including Acinetobacter baumannii can develop colistin resistance through a range of molecular mechanisms, some of which were characterized using Tn-seq. Furthermore, signal transduction pathways that regulate colistin resistance vary within Gram-negative bacteria. Here we propose an efficient method of transposon mutagenesis in A. baumannii that streamlines generation of a saturating transposon insertion library and amplicon library construction by eliminating the need for restriction enzymes, adapter ligation, and gel purification. The methods described herein will enable in-depth analysis of molecular determinants that contribute to A. baumannii fitness when challenged with colistin. The protocol is also applicable to other Gram-negative ESKAPE pathogens, which are primarily associated with drug resistant hospital-acquired infections.

A decade of advances in transposon-insertion sequencing

It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications.

In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.

Genetic determinants of Pseudomonas aeruginosa fitness during biofilm growth

Pseudomonas aeruginosa is an environmental bacterium and an opportunistic human pathogen. It is also a well-established model organism to study bacterial adaptation to stressful conditions, such as those encountered during an infection process in the human host. Advancing knowledge on P. aeruginosa adaptation to biofilm growth conditions is bound to reveal novel strategies and targets for the treatment of chronic biofilm-associated infections. Here, we generated transposon insertion libraries in three P. aeruginosa strain backgrounds and determined the relative frequency of each insertion following biofilm growth using transposon sequencing. We demonstrate that in general the SOS response, several tRNA modifying enzymes as well as adaptation to microaerophilic growth conditions play a key role in bacterial survival under biofilm growth conditions. On the other hand, presence of genes involved in motility and PQS signaling were less important during biofilm growth. Several mutants exhibiting transposon insertions in genes detected in our screen were validated for their biofilm growth capabilities and biofilm specific transcriptional responses using independently generated transposon mutants. Our results provide new insights into P. aeruginosa adaptation to biofilm growth conditions. The detection of previously unknown determinants of biofilm survival supports the use of transposon insertion sequencing as a global genomic technology for understanding the establishment of difficult to treat biofilm-associated infections.

Identification of genes required for the fitness of Streptococcus equi subsp. equi in whole equine blood and hydrogen peroxide

The availability of next-generation sequencing techniques provides an unprecedented opportunity for the assignment of gene function. Streptococcus equi subspecies equi is the causative agent of strangles in horses, one of the most prevalent and important diseases of equids worldwide. However, the live attenuated vaccines that are utilized to control this disease cause adverse reactions in some animals. Here, we employ transposon-directed insertion-site sequencing (TraDIS) to identify genes that are required for the fitness of S. equi in whole equine blood or in the presence of H2O2 to model selective pressures exerted by the equine immune response during infection. We report the fitness values of 1503 and 1471 genes, representing 94.5 and 92.5 % of non-essential genes in S. equi, following incubation in whole blood and in the presence of H2O2, respectively. Of these genes, 36 and 15 were identified as being important to the fitness of S. equi in whole blood or H2O2, respectively, with 14 genes being important in both conditions. Allelic replacement mutants were generated to validate the fitness results. Our data identify genes that are important for S. equi to resist aspects of the immune response in vitro, which can be exploited for the development of safer live attenuated vaccines to prevent strangles.

Application of Transposon Insertion Sequencing to Agricultural Science

Many plant-associated bacteria have the ability to positively affect plant growth and there is growing interest in utilizing such bacteria in agricultural settings to reduce reliance on pesticides and fertilizers. However, our capacity to utilize microbes in this way is currently limited due to patchy understanding of bacterial-plant interactions at a molecular level. Traditional methods of studying molecular interactions have sought to characterize the function of one gene at a time, but the slow pace of this work means the functions of the vast majority of bacterial genes remain unknown or poorly understood. New approaches to improve and speed up investigations into the functions of bacterial genes in agricultural systems will facilitate efforts to optimize microbial communities and develop microbe-based products. Techniques enabling high-throughput gene functional analysis, such as transposon insertion sequencing analyses, have great potential to be widely applied to determine key aspects of plant-bacterial interactions. Transposon insertion sequencing combines saturation transposon mutagenesis and high-throughput sequencing to simultaneously investigate the function of all the non-essential genes in a bacterial genome. This technique can be used for both in vitro and in vivo studies to identify genes involved in microbe-plant interactions, stress tolerance and pathogen virulence. The information provided by such investigations will rapidly accelerate the rate of bacterial gene functional determination and provide insights into the genes and pathways that underlie biotic interactions, metabolism, and survival of agriculturally relevant bacteria. This knowledge could be used to select the most appropriate plant growth promoting bacteria for a specific set of conditions, formulating crop inoculants, or developing crop protection products. This review provides an overview of transposon insertion sequencing, outlines how this approach has been applied to study plant-associated bacteria, and proposes new applications of these techniques for the benefit of agriculture.

A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni

The Gram-negative Epsilonproteobacterium Campylobacter jejuni is currently the most prevalent bacterial foodborne pathogen. Like for many other human pathogens, infection studies with C. jejuni mainly employ artificial animal or cell culture models that can be limited in their ability to reflect the in-vivo environment within the human host. Here, we report the development and application of a human three-dimensional (3D) infection model based on tissue engineering to study host-pathogen interactions. Our intestinal 3D tissue model is built on a decellularized extracellular matrix scaffold, which is reseeded with human Caco-2 cells. Dynamic culture conditions enable the formation of a polarized mucosal epithelial barrier reminiscent of the 3D microarchitecture of the human small intestine. Infection with C. jejuni demonstrates that the 3D tissue model can reveal isolate-dependent colonization and barrier disruption phenotypes accompanied by perturbed localization of cell-cell junctions. Pathogenesis-related phenotypes of C. jejuni mutant strains in the 3D model deviated from those obtained with 2D-monolayers, but recapitulated phenotypes previously observed in animal models. Moreover, we demonstrate the involvement of a small regulatory RNA pair, CJnc180/190, during infections and observe different phenotypes of CJnc180/190 mutant strains in 2D vs. 3D infection models. Hereby, the CJnc190 sRNA exerts its pathogenic influence, at least in part, via repression of PtmG, which is involved in flagellin modification. Our results suggest that the Caco-2 cell-based 3D tissue model is a valuable and biologically relevant tool between in-vitro and in-vivo infection models to study virulence of C. jejuni and other gastrointestinal pathogens.

Enteric pathogens have evolved numerous strategies to successfully colonize and persist in the human gastrointestinal tract. However, especially for the research of virulence mechanisms of human pathogens, often only limited infection models are available. Here, we have applied and further advanced a tissue-engineered human intestinal tissue model based on an extracellular matrix scaffold reseeded with human cells that can faithfully mimic pathogenesis-determining processes of the zoonotic pathogen Campylobacter jejuni. Our three-dimensional (3D) intestinal infection model allows for the assessment of epithelial barrier function during infection as well as for the quantification of bacterial adherence, internalization, and transmigration. Investigation of C. jejuni mutant strains in our 3D tissue model revealed isolate-specific infection phenotypes, in-vivo relevant infection outcomes, and uncovered the involvement of a small RNA pair during C. jejuni pathogenesis. Overall, our results demonstrate the power of tissue-engineered models for studying host-pathogen interactions, and our model will also be helpful to investigate other gastrointestinal pathogens.

Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes

While Tn-Seq is a powerful tool to determine genome-wide bacterial fitness in high-throughput, culturing transposon-mutant libraries in pools can mask community or other complex single-cell phenotypes. Droplet Tn-Seq (dTn-Seq) solves this problem by microfluidics facilitated encapsulation of individual transposon mutants into growth medium-in-oil droplets, thereby enabling isolated growth, free from the influence of the population. Here we describe and validate microfluidic chip design, production, encapsulation, and dTn-Seq sample preparation. We determine that 1-3% of mutants in Streptococcus pneumoniae have a different fitness when grown in isolation and show how dTn-Seq can help identify leads for gene function, including those involved in hyper-competence, processing of alpha-1-acid glycoprotein, sensitivity against the human leukocyte elastase and microcolony formation. Additionally, we show dTn-Seq compatibility with microscopy, FACS and investigations of bacterial cell-to-cell and bacteria-host cell interactions. dTn-Seq reduces costs and retains the advantages of Tn-Seq, while expanding the method's original applicability.

Transposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization

Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important food-borne pathogen that colonizes the colon. Transposon-insertion sequencing (TIS) was used to identify genes required for EHEC and E. coli K-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon. Surprisingly, many conserved loci contribute to EHEC's but not to K-12's growth in vitro. There was a restrictive bottleneck for EHEC colonization of the rabbit colon, which complicated identification of EHEC genes facilitating growth in vivo. Both a refined version of an existing analytic framework as well as PCA-based analysis were used to compensate for the effects of the infection bottleneck. These analyses confirmed that the EHEC LEE-encoded type III secretion apparatus is required for growth in vivo and revealed that only a few effectors are critical for in vivo fitness. Over 200 mutants not previously associated with EHEC survival/growth in vivo also appeared attenuated in vivo, and a subset of these putative in vivo fitness factors were validated. Some were found to contribute to efficient type-three secretion while others, including tatABC, oxyR, envC, acrAB, and cvpA, promote EHEC resistance to host-derived stresses. cvpA is also required for intestinal growth of several other enteric pathogens, and proved to be required for EHEC, Vibrio cholerae and Vibrio parahaemolyticus resistance to the bile salt deoxycholate, highlighting the important role of this previously uncharacterized protein in pathogen survival. Collectively, our findings provide a comprehensive framework for understanding EHEC growth in the intestine.

Genome-Wide Screening for Enteric Colonization Factors in Carbapenem-Resistant ST258 Klebsiella pneumoniae

A diverse, antibiotic-naive microbiota prevents highly antibiotic-resistant microbes, including carbapenem-resistant Klebsiella pneumoniae (CR-Kp), from achieving dense colonization of the intestinal lumen. Antibiotic-mediated destruction of the microbiota leads to expansion of CR-Kp in the gut, markedly increasing the risk of bacteremia in vulnerable patients. While preventing dense colonization represents a rational approach to reduce intra- and interpatient dissemination of CR-Kp, little is known about pathogen-associated factors that enable dense growth and persistence in the intestinal lumen. To identify genetic factors essential for dense colonization of the gut by CR-Kp, we constructed a highly saturated transposon mutant library with >150,000 unique mutations in an ST258 strain of CR-Kp and screened for in vitro growth and in vivo intestinal colonization in antibiotic-treated mice. Stochastic and partially reversible fluctuations in the representation of different mutations during dense colonization revealed the dynamic nature of intestinal microbial populations. We identified genes that are crucial for early and late stages of dense gut colonization and confirmed their role by testing isogenic mutants in in vivo competition assays with wild-type CR-Kp Screening of the transposon library also identified mutations that enhanced in vivo CR-Kp growth. These newly identified colonization factors may provide novel therapeutic opportunities to reduce intestinal colonization by CR-KpIMPORTANCEKlebsiella pneumoniae is a common cause of bloodstream infections in immunocompromised and hospitalized patients, and over the last 2 decades, some strains have acquired resistance to nearly all available antibiotics, including broad-spectrum carbapenems. The U.S. Centers for Disease Control and Prevention has listed carbapenem-resistant K. pneumoniae (CR-Kp) as an urgent public health threat. Dense colonization of the intestine by CR-Kp and other antibiotic-resistant bacteria is associated with an increased risk of bacteremia. Reducing the density of gut colonization by CR-Kp is likely to reduce their transmission from patient to patient in health care facilities as well as systemic infections. How CR-Kp expands and persists in the gut lumen, however, is poorly understood. Herein, we generated a highly saturated mutant library in a multidrug-resistant K. pneumoniae strain and identified genetic factors that are associated with dense gut colonization by K. pneumoniae This study sheds light on host colonization by K. pneumoniae and identifies potential colonization factors that contribute to high-density persistence of K. pneumoniae in the intestine.

The bare necessities: Uncovering essential and condition-critical genes with transposon sequencing

Querying gene function in bacteria has been greatly accelerated by the advent of transposon sequencing (Tn-seq) technologies (related Tn-seq strategies are known as TraDIS, INSeq, RB-TnSeq, and HITS). Pooled populations of transposon mutants are cultured in an environment and next-generation sequencing tools are used to determine areas of the genome that are important for bacterial fitness. In this review we provide an overview of Tn-seq methodologies and discuss how Tn-seq has been applied, or could be applied, to the study of oral microbiology. These applications include studying the essential genome as a means to rationally design therapeutic agents. Tn-seq has also contributed to our understanding of well-studied biological processes in oral bacteria. Other important applications include in vivo pathogenesis studies and use of Tn-seq to probe the molecular basis of microbial interactions. We also highlight recent advancements in techniques that act in synergy with Tn-seq such as clustered regularly interspaced short palindromic repeats (CRISPR) interference and microfluidic chip platforms.