Horizontal gene transfer and adaptive evolution in bacteria

Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits

One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bacterial genomes contain signatures of natural evolution and adaptive markers that can be exploited to better understand the behavior of pathogen in the food industry. The monitoring of foodborne strains can therefore be facilitated by the use of these genomic markers capable of rapidly providing essential information on isolated strains, such as the source of contamination, risk of illness, potential for biofilm formation, and tolerance or resistance to biocides. The increasing availability of large genome datasets is enhancing the understanding of the genetic basis of complex traits such as host adaptation, virulence, and persistence. Genome-wide association studies have shown very promising results in the discovery of genomic markers that can be integrated into rapid detection tools. In addition, machine learning has successfully predicted phenotypes and classified important traits. Genome-wide association and machine learning tools have therefore the potential to support decision-making circuits intending at reducing the burden of foodborne diseases. The aim of this chapter review is to provide knowledge on the use of these two methods in food microbiology and to recommend their use in the field.

Phylogenomic analysis uncovers an unexpected capacity for the biosynthesis of secondary metabolites in Pseudoalteromonas

Pseudoalteromonas is a genus of marine bacteria and a promising source of natural products with antibacterial, antifungal, and antifouling bioactivities. To accelerate the exploration of new compounds from this genus, we applied the gene-first approach to study 632 public Pseudoalteromonas genomes. We identified 3968 biosynthetic gene clusters (BGCs) involved in the biosynthesis of secondary metabolites and classified them into 995 gene cluster families (GCFs). Surprisingly, only 9 GCFs (0.9 %) included an experimentally identified reference biosynthetic gene cluster from the Minimum Information about a Biosynthetic Gene cluster database (MIBiG), suggesting a striking novelty of secondary metabolites in Pseudoalteromonas. Bioinformatic analysis of the biosynthetic diversity encoded in the identified BGCs uncovered six dominant species of this genus, P. citrea, P. flavipulchra, P. luteoviolacea, P. maricaloris, P. piscicida, and P. rubra, that encoded more than 17 BGCs on average. Moreover, each species exhibited a species-specific distribution of BGC. However, a deep analysis revealed two BGCs conserved across five of the six dominant species. These BGCS encoded an unknown lanthipeptide and the siderophore myxochelin B implying an essential role of antibiotics for Pseudoalteromonas. We chemically profiled 11 strains from the 6 dominant species and identified four new antibiotics, korormicins L-O (1-4), from P. citrea WJX-3. Our results highlight the unexplored biosynthetic potential for bioactive compounds in Pseudoalteromonas and provide an important guideline for targeting exploration.

Sneaky tactics: Ingenious immune evasion mechanisms of Bartonella

Gram-negative Bartonella species are facultative intracellular bacteria that can survive in the harsh intracellular milieu of host cells. They have evolved strategies to evade detection and degradation by the host immune system, which ensures their proliferation in the host. Following infection, Bartonella alters the initial immunogenic surface-exposed proteins to evade immune recognition via antigen or phase variation. The diverse lipopolysaccharide structures of certain Bartonella species allow them to escape recognition by the host pattern recognition receptors. Additionally, the survival of mature erythrocytes and their resistance to lysosomal fusion further complicate the immune clearance of this species. Certain Bartonella species also evade immune attacks by producing biofilms and anti-inflammatory cytokines and decreasing endothelial cell apoptosis. Overall, these factors create a challenging landscape for the host immune system to rapidly and effectively eradicate the Bartonella species, thereby facilitating the persistence of Bartonella infections and creating a substantial obstacle for therapeutic interventions. This review focuses on the effects of three human-specific Bartonella species, particularly their mechanisms of host invasion and immune escape, to gain new perspectives in the development of effective diagnostic tools, prophylactic measures, and treatment options for Bartonella infections.

Streptococcus suis serotype 4: a population with the potential pathogenicity in humans and pigs

Streptococcus suis is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different S. suis serotypes exhibit diverse characteristics in population structure and pathogenicity. Surveillance data highlight the significance of S. suis serotype 4 (SS4) in swine streptococcusis, a pathotype causing human infections. However, except for a few epidemiologic studies, the information on SS4 remains limited. In this study, we investigated the population structure, pathogenicity, and antimicrobial characteristics of SS4 based on 126 isolates, including one from a patient with septicemia. We discovered significant diversities within this population, clustering into six minimum core genome (MCG) groups (1, 2, 3, 4, 7-2, and 7-3) and five lineages. Two main clonal complexes (CCs), CC17 and CC94, belong to MCG groups 1 and 3, respectively. Numerous important putative virulence-associated genes are present in these two MCG groups, and 35.00% (7/20) of pig isolates from CC17, CC94, and CC839 (also belonging to MCG group 3) were highly virulent (mortality rate ≥ 80%) in zebrafish and mice, similar to the human isolate ID36054. Cytotoxicity assays showed that the human and pig isolates of SS4 strains exhibit significant cytotoxicity to human cells. Antimicrobial susceptibility testing showed that 95.83% of strains isolated from our labs were classified as multidrug-resistant. Prophages were identified as the primary vehicle for antibiotic resistance genes. Our study demonstrates the public health threat posed by SS4, expanding the understanding of SS4 population structure and pathogenicity characteristics and providing valuable information for its surveillance and prevention.

Key role of NH4+-N in the removal of oxacillin during managed aquifer recharge: Reconsidering the recharge limitation

Frequent occurrence of trace antibiotics in reclaimed water is concerning, which inevitably causes aquifer contamination in the case of managed aquifer recharge (MAR). Global governments have formulated strict reclaimed water standards to ensure the safety of water reuse. Recent studies have found that improved antibiotics removal is intimately associated with high ammonia-oxidizing activity. However, the role of NH4+-N in the removal of residual antibiotics of reclaimed water during MAR remains unknown. NH4+-N removal and the effects of ammonia oxidation on antibiotics biodegradation in the aquifer are the most significant facts for solving the above collision. In this work, the effects of NH4+-N (0, 1 and 5 mg/L) in a model refractory antibiotic (oxacillin (OXA), 100 μg/L) attenuation were deciphered by employing three individual simulated MAR columns, which so called N0, N1 and N5. The results showed that 5 mg/L NH4+-N in influent upregulated the abundance of amo genes by 28.9 %-68.0 % in N5. And the enriched functional genes encoding key degradation enzymes enhanced the OXA removal by 18.7 % and alleviated the oxidative stress caused by antibiotics. Subsequently, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) and human bacterial pathogens (HBPs) abundance were all significantly decreased. Moreover, the intimate association between ammonia-oxidizing microorganisms (AOM) and candidate OXA degraders based on microbial network analysis further supported the significance of AOM on OXA biodegradation. This study provides comprehensive evidence that appropriate amounts of NH4+-N are beneficial in antibiotics and antibiotic resistance risk reduction, providing compelling insights for refine NH4+-N recharge limitation.

Unveiling the role of uranium in enhancing the transformation of antibiotic resistance genes

Transformation represents one of the most important pathways for the horizontal transfer of antibiotic resistance genes (ARGs), which enables competent bacteria to acquire extracellular ARGs from the surrounding environment. Both heavy metals and irradiation have been demonstrated to influence the bacterial transformation process. However, the impact of ubiquitously occurring radioactive heavy metals on the transformation of ARGs remains largely unknown. Here, we showed that a representative radioactive nuclide, uranium (U), at environmental concentrations (0.005-5 mg/L), improved the transformation frequency of resistant plasmid pUC19 into Escherichia coli by 0.10-0.85-fold in a concentration-dependent manner. The enhanced ARGs transformation ability under U stress was demonstrated to be associated with reactive oxygen species (ROS) overproduction, membrane damage, and up-regulation of genes related to DNA uptake and recombination. Membrane permeability and ROS production were the predominant direct and indirect factors affecting transformation ability, respectively. Our findings provide valuable insight into the underlying mechanisms of the impacts of U on the ARGs transformation process and highlight concerns about the exacerbated spread of ARGs in radioactive heavy metal-contaminated ecosystems, especially in areas with nuclear activity or accidents.

Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation

Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.

Spatiotemporal dynamics of dinoflagellate communities in the Taiwan Strait and their correlations with micro-eukaryotic and bacterial communities

Dinoflagellate blooms have negative adverse effects on marine ecosystems. However, our knowledge about the spatiotemporal distribution of dinoflagellate communities and their correlations with micro-eukaryotic and bacterial communities is still rare. Here, the sediment micro-eukaryotic and bacterial communities were explored in the Taiwan Strait (TWS) by 16S and 18S rRNA gene high-throughput sequencing. We found that the dinoflagellates were the most abundant algal group in TWS, and their relative abundance was higher in spring and autumn than in summer. Moreover, the species richness and community composition of dinoflagellates showed strong seasonal patterns. NO3-N and NH4-N had the strongest correlations with the spatiotemporal dynamics of community composition of dinoflagellates. The dinoflagellates had a significantly wider niche breadth than other algal groups for NH4-N, NO3-N and NO2-N, and therefore potentially contributed to a wider distribution range and high abundance in TWS. In addition, the dinoflagellates had stronger impacts on microeukaryotes than on bacteria for both community composition and species richness. However, the dinoflagellates showed close coexistence with bacteria but loose coexistence with microeukaryotes in spring co-occurrence networks. This close coexistence suggests the potentially strong synergy effects between dinoflagellates and bacteria in spring dinoflagellate blooms in TWS. Overall, this study revealed the distribution mechanisms of dinoflagellates in TWS based on niche breadth and also unveiled the different effects of dinoflagellates on micro-eukaryotic and bacterial communities.

Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade

Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of Hypsibius henanensis sp. nov., we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (DODA1), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties. A tardigrade-specific radiation-induced disordered protein, TRID1, facilitates DNA damage repair through a mechanism involving phase separation. Two mitochondrial respiratory chain complex assembly proteins, BCS1 and NDUFB8, accumulate to accelerate nicotinamide adenine dinucleotide (NAD+) regeneration for poly(adenosine diphosphate-ribosyl)ation (PARylation) and subsequent poly(adenosine diphosphate-ribose) polymerase 1 (PARP1)-mediated DNA damage repair. These three observations expand our understanding of mechanisms of tardigrade radiotolerance.

Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools

The evolutionary arms race between bacteria and phages led to the emergence of bacterial immune systems whose diversity and dynamics remain poorly understood. Here we use comparative genomics to describe a widespread genetic element, defined by the presence of the Gamma-Mobile-Trio (GMT) proteins, that serves as a reservoir of offensive and defensive tools. We demonstrate, using Vibrio parahaemolyticus as a model, that GMT-containing genomic islands are active mobile elements. Furthermore, we show that GMT islands' cargoes contain various anti-phage defence systems, antibacterial type VI secretion system (T6SS) effectors and antibiotic-resistance genes. We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy. Our findings underscore the need to broaden the concept of 'defence islands' to include defensive and offensive tools, as both share the same mobile elements for dissemination.

Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations

Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.

Microevolution of Bartonella grahamii driven by geographic and host factors

Bartonella grahamii is one of the most prevalent Bartonella species in wild rodents and has been associated with human cases of neuroretinitis. The structure and distribution of genomic diversity in natural B. grahamii is largely unexplored. Here, we have applied a comprehensive population genomic and phylogenomic analysis to 172 strains of B. grahamii to unravel the genetic differences and influencing factors that shape its populations. The findings reveal a remarkable genomic diversity within the species, primarily in the form of single- nucleotide polymorphisms. The open pangenome of B. grahamii indicates a dynamic genomic evolution influenced by its ecological niche. Whole-genome data allowed us to decompose B. grahamii diversity into six phylogroups, each characterized by a unique "mosaic pattern" of hosts and biogeographic regions. This suggests a complex interplay between host specificity and biogeography. In addition, our study suggests a possible origin of European strains from Asian lineages, and host factors have a more significant impact on the genetic differentiation of B. grahamii than geographical factors. These insights contribute to understanding the evolutionary history of this pathogen and provide a foundation for future epidemiological research and public health strategies.

IMPORTANCE

Bartonella grahamii has been reported worldwide and shown to infect humans. Up to now, an effective transmission route of B. grahamii to humans has not been confirmed. The genetic evolution of B. grahamii and the relationship between B. grahamii and its host need to be further studied. The factors driving the genetic diversity of B. grahamii are still controversial. The results showed that the European isolates shared a common ancestor with the Chinese isolates. Host factors were shown to play an important role in driving the genetic diversity of B. grahamii. When host factors were fixed, geographic barriers drove B. grahamii microevolution. Our study emphasizes the importance of characterizing isolate genomes derived from hosts and geographical locations and provides a new reference for the origin of B. grahamii.

Nanomedicines as a cutting-edge solution to combat antimicrobial resistance

Antimicrobial resistance (AMR) poses a critical threat to global public health, necessitating the development of novel strategies. AMR occurs when bacteria, viruses, fungi, and parasites evolve to resist antimicrobial drugs, making infections difficult to treat and increasing the risk of disease spread, severe illness, and death. Over 70% of infection-causing microorganisms are estimated to be resistant to one or several antimicrobial drugs. AMR mechanisms include efflux pumps, target modifications (e.g., mutations in penicillin-binding proteins (PBPs), ribosomal subunits, or DNA gyrase), drug hydrolysis by enzymes (e.g., β-lactamase), and membrane alterations that reduce the antibiotic's binding affinity and entry. Microbes also resist antimicrobials through peptidoglycan precursor modification, ribosomal subunit methylation, and alterations in metabolic enzymes. Rapid development of new strategies is essential to curb the spread of AMR and microbial infections. Nanomedicines, with their small size and unique physicochemical properties, offer a promising solution by overcoming drug resistance mechanisms such as reduced drug uptake, increased efflux, biofilm formation, and intracellular bacterial persistence. They enhance the therapeutic efficacy of antimicrobial agents, reduce toxicity, and tackle microbial resistance effectively. Various nanomaterials, including polymeric-based, lipid-based, metal nanoparticles, carbohydrate-derived, nucleic acid-based, and hydrogels, provide efficient solutions for AMR. This review addresses the epidemiology of microbial resistance, outlines key resistance mechanisms, and explores how nanomedicines overcome these barriers. In conclusion, nanomaterials represent a versatile and powerful approach to combating the current antimicrobial crisis.

Microplastics-biofilm in aquatic ecosystem: Formation, pollutants complexation, greenhouse gas emission and ecotoxicology

The omnipresent microplastics (MPs) have gradually become a significant environmental problem due to its adverse consequences for ecological systems. MPs serve as substrates for biofilms colonization, which enhances adsorption of harmful contaminants on MPs surface in the aquatic ecosystem. The present study provides a critical discussion on the mechanism involved in MPs-biofilm formation, microbial colonization and the robust factors influencing the process in the aquatic ecosystem. Subsequently, the impact of MPs-biofilm on adsorption of inorganic and organic contaminants is explored. The ecological significance of MPs-biofilm associated pollutant complex for promoting greenhouse gases (GHGs) emissions from aquatic ecosystem is extensively discussed for understanding the climatic risk. Furthermore, the discussion is extended over ecotoxicological impact of MPs-biofilm on aquatic biodiversity and humans. The protective extracellular polymeric substances secreted by colonised bacteria over MPs during biofilm formation creates sticky MPs surface for heteroaggregates formation with swift adsorption of chemical compounds and microorganisms. MPs with functional aromatic groups facilitate the bacterial adhesion on the surface, but affect formation of biofilm. Alternatively, MPs-biofilm promotes the Mn and Fe hydrous oxides formation that can co-precipitate with heavy metal ions and facilitate in remediation measures. However, MPs biodegradation generates GHGs emission per unit mass, comparably more from freshwater than marine ecosystem. Considering the toxicity, MPs-biofilm induces the oxidative response in fishes, causing painful death and thus, destroys aquatic biodiversity. This study will be useful to address MPs-biofilm associated pollution scenario via trace, test and treat strategy involving future engineering research framework for ecological restoration.

Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history

Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.

Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance

The acquisition of multidrug resistance by pathogenic bacteria is a potentially incipient pandemic. Horizontal transfer of DNA from mobile integrative conjugative elements (ICEs) provides an important way to introduce genes that confer antibiotic (Ab)-resistance in recipient cells. Sizable numbers of SXT/R391 ICEs encode a hypermutagenic Rum DNA polymerase (Rum pol), which has significant homology with Escherichia coli pol V. Here, we show that even under tight transcriptional and post-transcriptional regulation imposed by host bacteria and the R391 ICE itself, Rum pol rapidly accelerates development of multidrug resistance (CIPR, RifR, AmpR) in E. coli in response to SOS-inducing Ab and non-Ab external stressors bleomycin (BLM), ciprofloxacin (CIP) and UV radiation. The impact of Rum pol on the rate of acquisition of drug resistance appears to surpass potential contributions from other cellular processes. We have shown that RecA protein plays a central role in controlling the ability of Rum pol to accelerate antibiotic resistance. A single amino acid substitution in RecA, M197D, acts as a 'Master Regulator' that effectively eliminates the Rum pol-induced Ab resistance. We suggest that Rum pol should be considered as one of the major factors driving development of de novo Ab resistance in pathogens carrying SXT/R391 ICEs.

Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer

Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.

A global genome dataset for Salmonella Gallinarum recovered between 1920 and 2024

Salmonella enterica serovar Gallinarum (S. Gallinarum) is an avian-specific pathogen responsible for fowl typhoid, a severe systemic disease with high mortality in chickens. This disease poses a substantial burden to the poultry industry, particularly in developing countries like China. However, comprehensive genome datasets on S. Gallinarum are lacking. Here, we present the most extensive S. Gallinarum genome dataset, comprising 574 well-collated samples. This dataset consists of 366 genomes sequenced in our laboratory and 208 publicly available genomes, collected from various continents over the past century. Using in silico prediction, we categorized S. Gallinarum into three distinct biovars. Regarding antimicrobial resistance, 238 strains (41.5%) carried antimicrobial resistance genes (ARGs) with a total of 635 records, while 232 strains (40.4%) exhibited multi-drug resistance. Mobile genomic elements (MGEs) serve as critical drivers for ARGs. Our dataset includes 5,636 MGEs records, with most MGEs belonging to prophages and plasmids. This dataset expands our understanding of the genomic characteristics of S. Gallinarum, providing valuable resources for future genomic studies to improve disease management.

Evolutionary origin and functional investigation of the widely conserved plant PEBP gene STEPMOTHER OF FT AND TFL1 (SMFT)

Genes of the family PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBP) have been intensely studied in plants for their role in cell (re)programming and meristem differentiation. Recently, sporadic reports of the presence of a new type of PEBP in plants became available, highly similar to the YY-PEBPs of prokaryotes. A comprehensive investigation of their spread, origin, and function revealed conservation across the plant kingdom. The YY-PEBP clade in plants seems to have resulted from a single Horizontal Gene Transfer (HGT) episode from a prokaryotic organism to an ancestral streptophyte. YY-PEBPs are also present in other eukaryotes, such as certain fungi, diatoms, and rotifers, and these cases derive from independent HGT events. Reciprocally, the occurrence of the eukaryotic CETS/RKIP type PEBPs (CR-PEBPs) was noticed in bacteria of the genus Nocardia, showing that HGT has occurred as well from eukaryotes to prokaryotes. Based on these observations, we propose that the current model of the PEBP family in plants needs to be updated with the clade STEPMOTHER OF FT AND TFL1 (SMFT). SMFT genes not only share high sequence conservation but also show specific expression in homologous plant structures that serve as propagules. Functional analysis of Arabidopsis smft mutant lines pointed to a function for this gene in regulating seed germination, both concerning primary dormancy release and in response to adverse high-temperature conditions. Overall, our study reveals an increasing complexity in the evolutionary history of the PEBP gene family, unlocking new potential in understanding the evolution and functional spectrum of these important key regulatory genes.

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance

The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.

Waterborne polyurethane nanoparticles incorporating linoleic acid as a potential strategy for controlling antibiotic resistance spread in the mammalian intestine

Plasmid-mediated conjugative transfer of antibiotic resistance genes (ARGs) within the human and animal intestine represents a substantial global health concern. linoleic acid (LA) has shown promise in inhibiting conjugation in vitro, but its in vivo effectiveness in the mammalian intestinal tract is constrained by challenges in efficiently reaching the target site. Recent advancements have led to the development of waterborne polyurethane nanoparticles for improved drug delivery. In this study, we synthesized four waterborne polyurethane nanoparticles incorporating LA (WPU@LA) using primary raw materials, including N-methyldiethanolamine, 2,2'-(piperazine-1,4-diyl) diethanol, isophorone diisocyanate, castor oil, and acetic acid. These nanoparticles, identified as WPU0.89@LA, WPU0.99@LA, WPU1.09@LA, and WPU1.19@LA, underwent assessment for their pH-responsive release property and biocompatibility. Among these, WPU0.99@LA displayed superior pH-responsive release properties and biocompatibility towards Caco-2 and IPEC-J2 cells. In a mouse model, a dosage of 10 mg/kg/day WPU0.99@LA effectively reduced the conjugation of IncX4 plasmids carrying the mobile colistin resistance gene (mcr-1) by more than 45.1-fold. In vivo toxicity assessment demonstrated that 10 mg/kg/day WPU0.99@LA maintains desirable biosafety and effectively preserves gut microbiota homeostasis. In conclusion, our study provides crucial proof-of-concept support, demonstrating that WPU0.99@LA holds significant potential in controlling the spread of antibiotic resistance within the mammalian intestine.

A global microbiome analysis reveals the ecological feature of Tistrella and its production of the bioactive didemnins in the marine ecosystem

Marine microorganisms like Tistrella are essential for producing bioactive compounds, including didemnins with antitumor and antiviral properties. However, our understanding of Tistrella's ecological features and didemnin production in natural environments is limited. In this study, we used genomics and metagenomics to show that Tistrella is widely distributed across natural habitats, especially in marine environments from the surface to 5000 m deep, with distinct non-random distribution patterns revealed by co-occurrence analysis. Importantly, transcriptional profiling of didemnin biosynthetic gene clusters indicates active in situ production of this compound within marine ecosystems. These findings enhance our understanding of Tistrella's ecology and secondary metabolite production in natural environments. Further research is needed to explore the ecological dynamics and functional impacts of Tistrella in these ecosystems.

Antibiotic Susceptibility Testing and Establishment of Tentative Species-Specific Microbiological Cut-off Values for Bifidobacteria Isolated from Chinese Population

Bifidobacteria are commonly used as probiotics in the food industry. The resistance of Bifidobacterium species to antibiotics is closely linked to food safety. However, we still lack a system for the safety evaluation of antibiotic resistance in bifidobacteria, and genus-level microbiological cut-off values remain in use for the determination of phenotypic resistance of Bifidobacterium strains to a given antibiotic. Here, we collected a total of 422 gut-derived bifidobacterial strains isolated from Chinese population and identified their phenotypic resistance profiles against ampicillin, amoxicillin, ciprofloxacin, chloramphenicol, clindamycin, erythromycin, rifampicin, tetracycline, trimethoprim, and vancomycin. Different Bifidobacterium species were found to have varying tolerances to the same antibiotic; therefore, we further established species-specific cut-off values for bifidobacterial species to ten antibiotics. Species-specific rather than genus-specific cut-off values for species belonging to the same taxon were considered more suitable to determine the phenotypic resistance of a Bifidobacterium strain. Moreover, a comprehensive scanning of antibiotic resistance genes in all Bifidobacterium strains tested revealed that the existence of the tetracycline resistance gene tet(W) and the erythromycin/clindamycin resistance gene ErmX is closely related to host phenotypes. Our findings provide guidance and reference values at both phenotype and genotype levels for the safe application of bifidobacteria in the food industry and the development of probiotic resistance evaluation standards.

Efficient reduction of antibiotic resistance genes and mobile genetic elements in organic waste composting via fenton-like treatment

Livestock manure harbors antibiotic resistance genes (ARGs), and aerobic composting (AC) is widely adopted for waste management. However, mitigating ARG resurgence in later stages remains challenging. This work aims to curb ARGs rebounding through a Fenton-like reaction during food waste and swine manure co-composting. Results revealed that 0.025 % zerovalent iron (ZVI) + 0.5 % hydrogen peroxide (H2O2) facilitated maximum ARG, mobile genetic elements (MGEs), and 16 s rRNA removal with reductions of 2.68, 2.69, and 1.4 logs. Spectroscopic analysis confirmed Fenton-like reaction and cell apoptosis analysis indicated that 0.025 % ZVI and 0.5 % H2O2 treatment had the maximum early apoptosis, least observed, and normal cells on day 30. Redundancy analysis highlighted the influence of bacterial communities and physicochemical properties on ARGs, with MGEs playing a crucial role in Fenton treatments. Our findings suggest incorporating ZVI and H2O2 in composting can significantly reduce ARGs and enhance waste management practices.

A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus

Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (KanR) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (KanR) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.

Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis

Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.

An Overview of the Recent Advances in Antimicrobial Resistance

Antimicrobial resistance (AMR), frequently considered a major global public health threat, requires a comprehensive understanding of its emergence, mechanisms, advances, and implications. AMR's epidemiological landscape is characterized by its widespread prevalence and constantly evolving patterns, with multidrug-resistant organisms (MDROs) creating new challenges every day. The most common mechanisms underlying AMR (i.e., genetic mutations, horizontal gene transfer, and selective pressure) contribute to the emergence and dissemination of new resistant strains. Therefore, mitigation strategies (e.g., antibiotic stewardship programs-ASPs-and infection prevention and control strategies-IPCs) emphasize the importance of responsible antimicrobial use and surveillance. A One Health approach (i.e., the interconnectedness of human, animal, and environmental health) highlights the necessity for interdisciplinary collaboration and holistic strategies in combating AMR. Advancements in novel therapeutics (e.g., alternative antimicrobial agents and vaccines) offer promising avenues in addressing AMR challenges. Policy interventions at the international and national levels also promote ASPs aiming to regulate antimicrobial use. Despite all of the observed progress, AMR remains a pressing concern, demanding sustained efforts to address emerging threats and promote antimicrobial sustainability. Future research must prioritize innovative approaches and address the complex socioecological dynamics underlying AMR. This manuscript is a comprehensive resource for researchers, policymakers, and healthcare professionals seeking to navigate the complex AMR landscape and develop effective strategies for its mitigation.

DdmDE eliminates plasmid invasion by DNA-guided DNA targeting

Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.

Nanoscale zero-valent iron alleviated horizontal transfer of antibiotic resistance genes in soil: The important role of extracellular polymeric substances

Extracellular polymeric substances (EPS) are tightly related to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), but often neglected in soil. In this study, nanoscale zero-valent iron (nZVI) was utilized for attenuation of ARGs in contaminated soil, with an emphasis on its effects on EPS secretion and HGT. Results showed during soil microbe cultivation exposed to tetracycline, more EPS was secreted and significant increase of tet was observed due to facilitated HGT. Notably, copies of EPS-tet accounted for 71.39 % of the total tet, implying vital effects of EPS on ARGs proliferation. When co-exposed to nZVI, EPS secretion was decreased by 38.36-71.46 %, for that nZVI could alleviate the microbial oxidative stress exerted by tetracycline resulting in downregulation of genes expression related to the c-di-GMP signaling system. Meanwhile, the abundance of EPS-tet was obviously reduced from 7.04 to 5.12-6.47 log unit, directly causing decrease of total tet from 7.19 to 5.68-6.69 log unit. For the reduced tet, it was mainly due to decreased EPS secretion induced by nZVI resulting in inhibition of HGT especially transformation of the EPS-tet. This work gives an inspiration for attenuation of ARGs dissemination in soil through an EPS regulation strategy.

Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in host Casuarina equisetifolia

Introduction

Casuarina equisetifolia is a common protective forest in coastal areas. However, artificial C. equisetifolia forests cannot self-renew, mainly due to the accumulation of allelochemicals. Endophytic bacteria may alleviate the root growth inhibition caused by allelochemicals in C. equisetifolia seedlings. B. amyloliquefaciens and B. aryabhattai were endophytic bacteria with strong allelopathy in C. equisetifolia root. The allelopathy mechanism of these two endophytes and their interaction with C. equisetifolia remains to be studied.

Methods

Whole-genome sequencing of B. amyloliquefaciens and B. aryabhattai isolated from the roots of allelochemical-accumulating C. equisetifolia was performed using Illumina Hiseq and PacBio single-molecule sequencing platforms. Sterile seedlings of C. equisetifolia were treated with either individual or mixed bacterial cultures through root drenching. Transcriptional and metabolomics analyses were conducted after 3 days of infection.

Results and discussion

Whole-genome sequencing of Bacillus aryabhattai and Bacillus amyloliquefaciens showed that the two strains contained various horizontal gene transfer elements such as insertion sequence, prophage and transposon. In addition, these two strains also contain numerous genes related to the synthesis and catabolism of allelochemicals. After these two strains of bacteria were individually or mixed infected with C. equisetifolia, metabolomics and transcriptomic analysis of C. equisetifolia showed the 11 important secondary metabolite biosynthesis among them alkaloids biosynthesis, phenylpropanoid and terpenes biosynthesis and related genes were putatively regulated. Correlation analysis revealed that 48 differentially expressed genes had strong positive correlations with 42 differential metabolites, and 48 differentially expressed genes had strong negative correlations with 36 differential metabolites. For example, CMBL gene showed positive correlations with the allelochemical (-)-Catechin gallate, while Bp10 gene showed negative correlations with (-)-Catechin gallate.

Conclusion

The intergenerational accumulation of allelochemicals may induce horizontal gene transfer in endogenic bacteria of Casuarina equisetifolia root. Endophytic Bacillus plays an allelopathic role by assisting the host in regulating gene expression and the production and/or variety of allelochemicals. This comprehensive study sheds light on the intricate genetic and metabolic interactions between Bacillus endophytes and C. equisetifolia. These findings provide insights into endophyte-mediated allelopathy and its potential uses in plant biology and forest sustainability.

Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica

The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64T, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m-2 s-1, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m-2 s-1) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

IMPORTANCE

Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.

Microbial genotoxin-elicited host DNA mutations related to mitochondrial dysfunction, a momentous contributor for colorectal carcinogenesis

Gut microbe dysbiosis increases repetitive inflammatory responses, leading to an increase in the incidence of colorectal cancer. Recent studies have revealed that specific microbial species directly instigate mutations in the host nucleus DNA, thereby accelerating the progression of colorectal cancer. Given the well-established role of mitochondrial dysfunction in promoting colorectal cancer, it is reasonable to postulate that gut microbes may induce mitochondrial gene mutations, thereby inducing mitochondrial dysfunction. In this review, we focus on gut microbial genotoxins and their known and potential targets in mitochondrial genes. Consequently, we propose that targeted disruption of genotoxin transport pathways may effectively reduce the rate of mitochondrial gene mutations and yield substantial benefits for the prevention of colorectal carcinogenesis.

DNA Molecular Glue Assisted Bacterial Conjugative Transfer

Bacterial conjugation, a commonly used method to horizontally transfer functional genes from donor to recipient strains, plays an important role in the genetic manipulation of bacteria for basic research and industrial production. Successful conjugation depends on the donor-recipient cell recognition and a tight mating junction formation. However, the efficiency of conjugative transfer is usually very low. In this work, we developed a new technique that employed DNA molecule "glue" to increase the match frequency and the interaction stability between the donor and recipient cells. We used two E. coli strains, ETZ and BL21, as a model system, and modified them with the complementary ssDNA oligonucleotides by click chemistry. The conjugation efficiency of the modified bacteria was improved more than 4 times from 10 %-46 %. This technique is simple and generalizable as it only relies on the active amino groups on the bacterial surface. It is expected to have broad applications in constructing engineered bacteria.

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state ("status quo") and future directions ("quo vadis") based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens. The future directions include the application of new techniques, such as machine learning and network approaches that may overcome the current shortcomings. These include the use of fixed genomic distances in cluster delineation, disentangling similarity or lack thereof in source attribution, and difficulties ascertaining function in hazard characterization. Although, the aforementioned methods can relatively easily be applied technically, an overarching challenge is the inference and biological/epidemiological interpretation of these large amounts of high-resolution data. Understanding the context in terms of bacterial isolate and host diversity allows to assess the level of representativeness in regard to sources and isolates in the dataset, which in turn defines the level of certainty associated with defining clusters, sources and risks. This also marks the importance of metadata (clinical, epidemiological, and biological) when using genomics for public health purposes.

Streptococcus dysgalactiae subsp. equisimilis infection and its intersection with Streptococcus pyogenes

SUMMARYStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen, Streptococcus pyogenes. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and S. pyogenes, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with S. pyogenes. In doing so, we highlight the importance of understanding the overlap of SDSE and S. pyogenes to inform surveillance and disease control strategies.

Staphylococcus capitis: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species

SUMMARYStaphylococcus capitis is divided into two subspecies, S. capitis subsp. ureolyticus (renamed urealyticus in 1992; ATCC 49326) and S. capitis subsp. capitis (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). S. capitis is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying S. capitis pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to S. capitis genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for S. capitis in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of S. capitis among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.

Reticulate evolution: Detection and utility in the phylogenomics era

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

Networking the desert plant microbiome, bacterial and fungal symbionts structure and assortativity in co-occurrence networks

In nature, microbes do not thrive in seclusion but are involved in complex interactions within- and between-microbial kingdoms. Among these, symbiotic associations with mycorrhizal fungi and nitrogen-fixing bacteria are namely known to improve plant health, while providing resources to benefit other microbial members. Yet, it is not clear how these microbial symbionts interact with each other or how they impact the microbiota network architecture. We used an extensive co-occurrence network analysis, including rhizosphere and roots samples from six plant species in a natural desert in AlUla region (Kingdom of Saudi Arabia) and described how these symbionts were structured within the plant microbiota network. We found that the plant species was a significant driver of its microbiota composition and also of the specificity of its interactions in networks at the microbial taxa level. Despite this specificity, a motif was conserved across all networks, i.e., mycorrhizal fungi highly covaried with other mycorrhizal fungi, especially in plant roots-this pattern is known as assortativity. This structural property might reflect their ecological niche preference or their ability to opportunistically colonize roots of plant species considered non symbiotic e.g., H. salicornicum, an Amaranthaceae. Furthermore, these results are consistent with previous findings regarding the architecture of the gut microbiome network, where a high level of assortativity at the level of bacterial and fungal orders was also identified, suggesting the existence of general rules of microbiome assembly. Otherwise, the bacterial symbionts Rhizobiales and Frankiales covaried with other bacterial and fungal members, and were highly structural to the intra- and inter-kingdom networks. Our extensive co-occurrence network analysis of plant microbiota and study of symbiont assortativity, provided further evidence on the importance of bacterial and fungal symbionts in structuring the global plant microbiota network.

Graphite: painting genomes using a colored de Bruijn graph

The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling the tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands of matches that are tedious to interpret and pose computational challenges. We developed Graphite that uses a colored de Bruijn graph (cDBG) to paint query genomes, selecting the local best matches along the full query length. By focusing on the best genomic match of each query region, Graphite reduces the number of matches while providing the most promising leads for sequence tracking or genomic forensics. When applied to hundreds of Campylobacter genomes we found extensive gene sharing, including a previously undetected C. coli plasmid that matched a C. jejuni chromosome. Together, genome painting using cDBGs as enabled by Graphite, can reveal new biological phenomena by mitigating computational hurdles.

The genetic diversity and evolution analysis of the Hainan melioidosis outbreak strains

Melioidosis is a zoonotic disease, with its outbreaks being rare and indicative of an unusual concurrence of extreme climate and natural environmental factors. An outbreak of melioidosis cases emerged in Hainan following Typhoon "Dianmu" from October to December 2021, presenting an opportunity to identify the environmental sources of infection for these cases due to its nature as a well-defined point-source cluster. To investigate the relationship between the occurrence of these melioidosis cases and the environment, we extracted the entire genome of 25 clinical strains and conducted MLST typing, followed by whole genome sequencing and analysis of molecular genetic information for four ST46 genotypes from these strains. Phylogenetic and evolutionary relationships between Hainan sequence types (STs) and those found in other endemic regions were analyzed using IslandPath-DIMO, PHASTER, e-BURST, PHYLOViZ, and the maximum likelihood method. Notably, a total of 25 clinical strains were identified, encompassing 12 STs (ST46, ST1105, ST1991, ST30, ST1992, ST50, ST164, ST55, ST70, ST1993, ST1545, and ST58), with ST1991, ST1992, and ST1993 being newly discovered subtypes. PHYLOViZ clustering analysis divided the strains into two groups (A and B), both closely related to the Asian region. Phylogenetic tree analysis further revealed that most of the strains in this study were closely related to those found in Australia and Thailand. Analysis of patient information and visits to their residences suggested that contaminated water sources might be the primary source of infection during this outbreak. Our findings underscore that extreme weather events, such as typhoons, significantly increase the infection rate of B. pseudomallei, along with its genetic diversity, necessitating additional prevention strategies to control these B. pseudomallei infections.

Adaptive strategies and ecological roles of phages in habitats under physicochemical stress

Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.

The evolution of autonomy from two cooperative specialists in fluctuating environments

From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.

An Exopolysaccharide from the Cyanobacterium Arthrospira platensis May Utilize CH-π Bonding: A Review of the Isolation, Purification, and Chemical Structure of Calcium-Spirulan

The CH-π bonding potential of a saccharide is determined primarily by the number of hydrogen atoms available for bonding and is reduced by side groups that interfere with the CH-π bond. Each hydrogen bond increases the total bond energy, while interfering hydroxyl groups and other side groups reduce the bond energy by repulsion. The disaccharide repeating units of Calcium-Spirulan (Ca-SP), a large exopolysaccharide sub fractionated from the supernatant of the cyanobacterium Arthrospira platensis, contain a unique monosaccharide that is completely devoid of hydroxyl groups and side groups on its entire beta surface, leaving five hydrogen atoms available for CH-π bonding in the planar conformation. While planar conformations of independent pyranose rings are rare-to-nonexistent, due to ring strain associated with that conformation, the binding site of a protein could provide the conformational energy needed to overcome that energy barrier. By enabling a planar conformation, a protein could also enable the sugar to form a novel 5-hydrogen CH-π bond configuration. One study of the anticoagulant property of Ca-SP shows that the molecule acts as an activator of Heparin Cofactor II (HC-II), boosting its anticoagulant kinetics by 104. In comparison, the longstanding anticoagulant drug Heparin boosts the HC-II kinetics by 103. The difference may be explained by this unique CH-π configuration. Here, we review current knowledge and experience on the isolation techniques, analytical methods, and chemical structures of Ca-SP. We emphasize a discussion of the CH-π bonding potential of this unique polysaccharide because it is a topic that has not yet been addressed. By introducing the topic of CH-π bonding to the cyanobacterial research community, this review may help to set the stage for further investigation of these unique molecules, their genetics, their biosynthetic pathways, their chemistry, and their biological functions.

Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome

Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.

Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes

Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.

Disinfection and post-disinfection conditions drive bacterial and viral evolution across the environment and host

Water disinfection practices have long been established as a critical engineering intervention for controlling pathogen transmission and safeguarding individual and public health. However, recent discoveries have unveiled the significant role disinfection and post-disinfection play in accelerating the development of resistance to disinfectants and antimicrobial drugs within bacterial and viral communities in the environment. This phenomenon, in turn, may facilitate the emergence of persistent microbes and those with new genetic characteristics. These microbes may thrive in host environments with increased infectivity and resistance, posing challenges to current medical treatments and jeopardizing human health. In this perspective, we illuminate the intricate interplay between aquatic environments, microbes, and hosts and how microbial virulence evolves across the environment and host under the pressure of disinfection and post-disinfection conditions. We aim to draw attention to the previously overlooked potential risks associated with disinfection in driving the virulence evolution of bacteria and viruses, establish connections between pathogens in diverse environments and hosts within the overarching framework of the One Health concept, and ultimately provide guidelines for advancing future water disinfection technologies to effectively curb the spread of infectious diseases.

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Bacterial evolution in Biofiltration of drinking water treatment plant: Different response of phage and plasmid to varied water sources

Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies.

Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.

Regulation of intracellular process by two-component systems: Exploring the mechanism of plasmid-mediated conjugative transfer

Plasmid-mediated conjugative transfer facilitates the dissemination of antibiotic resistance, yet the comprehensive regulatory mechanisms governing this process remain elusive. Herein, we established pure bacteria and activated sludge conjugation system to investigate the regulatory mechanisms of conjugative transfer, leveraging metformin as an exogenous agent. Transcriptomic analysis unveiled that substantial upregulation of genes associated with the two-component system (e.g., AcrB/AcrA, EnvZ/Omp, and CpxA/CpxR) upon exposure to metformin. Furthermore, downstream regulators of the two-component system, including reactive oxygen species (ROS), cytoplasmic membrane permeability, and adenosine triphosphate (ATP) production, were enhanced by 1.7, 1.4 and 1.1 times, respectively, compared to the control group under 0.1 mg/L metformin exposure. Moreover, flow sorting and high-throughput sequencing revealed increased microbial community diversity among transconjugants in activated sludge systems. Notably, the antibacterial potential of human pathogenic bacteria (e.g., Bacteroides, Escherichia-Shigella, and Lactobacillus) was augmented, posing a potential threat to human health. Our findings shed light on the spread of antibiotic resistance bacteria and assess the ecological risks associated with plasmid-mediated conjugative transfer in wastewater treatment systems.