Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene

Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities

Rapid advancements in long-read sequencing have facilitated species-level microbial profiling through full-length 16S rRNA sequencing (~ 1500 bp), and more notably, by the newer 16S-ITS-23S ribosomal RNA operon (RRN) sequencing (~ 4500 bp). RRN sequencing is emerging as a superior method for species resolution, exceeding the capabilities of short-read and full-length 16S rRNA sequencing. However, being in its early stages of development, RRN sequencing has several underexplored or understudied elements, highlighting the need for a critical and thorough examination of its methodologies. Key areas that require detailed analysis include understanding how primer pairs, sequencing platforms, and classifiers and databases affect the accuracy of species resolution achieved through RRN sequencing. Our study addresses these gaps by evaluating the effect of primer pairs using four RRN primer combinations, and that of sequencing platforms by employing PacBio and Oxford Nanopore Technologies (ONT) systems. Furthermore, two classification methods (Minimap2 and OTU clustering), in combination with four RRN reference databases (MIrROR, rrnDB, and two versions of GROND) were compared to identify consistent and accurate classification methods with RRN sequencing. Here we demonstrate that RRN primer pair choice and sequencing platform do not substantially bias taxonomic profiles for most of the tested mock communities, while classification methods significantly impact the accuracy of species-level assignments. Of the classification methods tested, Minimap2 classifier in combination with the GROND database most consistently provided accurate species-level classification across the communities tested, irrespective of sequencing platform.

We are doing it wrong: Putting homology before phylogeny in cyanobacterial taxonomy

The rapid expansion of whole genome sequencing in bacterial taxonomy has revealed deep evolutionary relationships and speciation signals, but assembly methods often miss true nucleotide diversity in the ribosomal operons. Though it lacks sufficient phylogenetic signal at the species level, the 16S ribosomal RNA gene is still much used in bacterial taxonomy. In cyanobacterial taxonomy, comparisons of 16S-23S Internal Transcribed Spacer (ITS) regions are used to bridge this information gap. Although ITS rRNA region analyses are routinely being used to identify species, researchers often do not identify orthologous operons, which leads to improper comparisons. No method for delineating orthologous operon copies from paralogous ones has been established. A new method for recognizing orthologous ribosomal operons by quantifying the conserved paired nucleotides in a helical domain of the ITS, has been developed. The D1' Index quantifies differences in the ratio of pyrimidines to purines in paired nucleotide sequences of this helix. Comparing 111 operon sequences from 89 strains of Brasilonema, four orthologous operon types were identified. Plotting D1' Index values against the length of helices produced clear separation of orthologs. Most orthologous operons in this study were observed both with and without tRNA genes present. We hypothesize that genomic rearrangement, not gene duplication, is responsible for the variation among orthologs. This new method will allow cyanobacterial taxonomists to utilize ITS rRNA region data more correctly, preventing erroneous taxonomic hypotheses. Moreover, this work could assist genomicists in identifying and preserving evident sequence variability in ribosomal operons, which is an important proxy for evolution in prokaryotes.

The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification

The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.

Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.

Evaluation of the genetic stability of Leptospira reference strains maintained under two conservation methods

Objective. The genetic stability of Strains of Leptospira spp., maintained under two conservation systems, was evaluated. Methodology. The degree of conservation of the 16S rRNA and ompL1 genes of 10 reference serovars from the Leptospira spp. collection, belonging to the Sistema de Bancos de Germoplasma de la Nación para la Alimentación y la Agricultura (SBGNAA), was determined. Results. It was corroborated that the genes evaluated these have not undergone considerable changes, since similarities greater than 99.69 % were evidenced for 16S rRNA and 99.02% for ompL1, in the paired alignments. Conclusion. The genetic stability and purity of the reference strains of Leptospira spp. were verified. spp., kept in cryopreservation in liquid nitrogen at -196 °C and at room temperature for approximately eight years.

DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.

Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

BACKGROUND

The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].

RESULTS

At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).

CONCLUSIONS

Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.

Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence

Recent development of long-read sequencing platforms has enabled researchers to explore bacterial community structure through analysis of full-length 16S rRNA gene (∼1,500 bp) or 16S-ITS-23S rRNA operon region (∼4,300 bp), resulting in higher taxonomic resolution than short-read sequencing platforms. Despite the potential of long-read sequencing in metagenomics, resources and protocols for this technology are scarce. Here, we describe MIrROR, the database and analysis tool for metataxonomics using the bacterial 16S-ITS-23S rRNA operon region. We collected 16S-ITS-23S rRNA operon sequences extracted from bacterial genomes from NCBI GenBank and performed curation. A total of 97,781 16S-ITS-23S rRNA operon sequences covering 9,485 species from 43,653 genomes were obtained. For user convenience, we provide an analysis tool based on a mapping strategy that can be used for taxonomic profiling with MIrROR database. To benchmark MIrROR, we compared performance against publicly available databases and tool with mock communities and simulated data sets. Our platform showed promising results in terms of the number of species covered and the accuracy of classification. To encourage active 16S-ITS-23S rRNA operon analysis in the field, BLAST function and taxonomic profiling results with 16S-ITS-23S rRNA operon studies, which have been reported as BioProject on NCBI are provided. MIrROR (http://mirror.egnome.co.kr/) will be a useful platform for researchers who want to perform high-resolution metagenome analysis with a cost-effective sequencer such as MinION from Oxford Nanopore Technologies. IMPORTANCE Metabarcoding is a powerful tool to investigate community diversity in an economic and efficient way by amplifying a specific gene marker region. With the advancement of long-read sequencing technologies, the field of metabarcoding has entered a new phase. The technologies have brought a need for development in several areas, including new markers that long-read can cover, database for the markers, tools that reflect long-read characteristics, and compatibility with downstream analysis tools. By constructing MIrROR, we met the need for a database and tools for the 16S-ITS-23S rRNA operon region, which has recently been shown to have sufficient resolution at the species level. Bacterial community analysis using the 16S-ITS-23S rRNA operon region with MIrROR will provide new insights from various research fields.

Native and foreign mitochondrial and nuclear encoded proteins conform the OXPHOS complexes of a holoparasitic plant

The intimate contact between the holoparasitic plant Lophophytum mirabile (Balanophoraceae) and its host plant (Fabaceae) facilitates the exchange of genetic information, increasing the frequency of horizontal gene transfer (HGT). Lophophytum stands out because it acquired a large number of mitochondrial genes (greater than 20) from its legume host that replaced the majority of the native homologs. These foreign genes code for proteins that form multisubunit enzyme complexes, such as those in the oxidative phosphorylation system (OXPHOS) and cytochrome c maturation (ccm) system, together with dozens of nuclear-encoded subunits. However, the existence and the origin of the nuclear subunits that form the major part of the OXPHOS and ccm system in Lophophytum remain unknown. It was proposed that nuclear-encoding genes whose products interact with foreign mitochondrial proteins are also foreign, minimizing the incompatibilities that could arise in the assembly and functioning of these multiprotein complexes. We identified a nearly complete set of OXPHOS and ccm system subunits evolving under selective constraints in the transcriptome of Lophophytum, indicating that OXPHOS is functional and resembles that of free-living angiosperms. Maximum Likelihood phylogenetic analyses revealed a single case of HGT in the nuclear genes, which results in mosaic OXPHOS and ccm system in Lophophytum. These observations raise new questions about the evolution and physiology of this parasitic plant. A putative case of cooperation between two foreign (one mitochondrial and one nuclear) genes is presented.

Relation between two evolutionary clocks reveal new insights in bacterial evolution

New insights in evolution are available thanks to next-generation sequencing technologies in recent years. However, due to the network of complex relations between species, caused by the intensive horizontal gene transfer (HGT) between different bacterial species, it is difficult to discover bacterial evolution. This difficulty leads to new research in the field of phylogeny, including the gene-based phylogeny, in contrast to sequence-based phylogeny. In previous articles, we presented evolutionary insights of Synteny Index (SI) study on a large biological dataset. We showed that the SI approach naturally clusters 1133 species into 39 cliques of closely related species. In addition, we presented a model that enables calculation of the number of translocation events between genomes based on their SI distance. Here, these two studies are combined together and lead to new insights. A principal result is the relation between two evolutionary clocks: the well-known sequence-based clock influenced by point mutations, and SI distance clock influenced by translocation events. A surprising linear relation between these two evolutionary clocks rising for closely related species across all genus. In other words, these two different clocks are ticking at the same rate inside the genus level. Conversely, a phase-transition manner discovered between these two clocks across non-closely related species. This may suggest a new genus definition based on an analytic approach, since the phase-transition occurs where each gene, on average, undergoes one translocation event. In addition, rare cases of HGT among highly conserved genes can be detected as outliers from the phase-transition pattern.

A positive correlation between GC content and growth temperature in prokaryotes

BACKGROUND

GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate.

RESULTS

With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation.

CONCLUSIONS

This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

The mosquito microbiome includes habitat-specific but rare symbionts

Microbial communities are known to influence mosquito lifestyles by modifying essential metabolic and behavioral processes that affect reproduction, development, immunity, digestion, egg survival, and the ability to transmit pathogens. Many studies have used 16S rRNA gene amplicons to characterize mosquito microbiota and investigate factors that influence host-microbiota dynamics. However, a relatively low taxonomic resolution due to clustering methods based on arbitrary threshold and the overall dominance of Wolbachia or Asaia symbionts obscured the investigation of rare members of mosquito microbiota in previous studies. Here, we used high resolution Shannon entropy-based oligotyping approach to analyze the microbiota of Culex pipiens, Culex quinquefasciatus and Aedes individuals from continental Southern France and overseas Guadeloupe as well as from laboratories with or without antibiotics treatment. Our experimental design that resulted in a series of mosquito samples with a gradient of Wolbachia density and relative abundance along with high-resolution analyses of amplicon sequences enabled the recovery of a robust signal from typically less accessible bacterial taxa. Our data confirm species-specific mosquito-bacteria associations with geography as a primary factor that influences bacterial community structure. But interestingly, they also reveal co-occurring symbiotic bacterial variants within single individuals for both Elizabethkingia and Erwinia genera, distinct and specific Asaia and Chryseobacterium in continental and overseas territories, and a putative rare Wolbachia variant. Overall, our study reveals the presence of previously overlooked microdiversity and multiple closely related symbiotic strains within mosquito individuals with a remarkable habitat-specificity.

Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.

Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit

OBJECTIVES

Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU).

METHODS

Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing.

RESULTS

Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%).

CONCLUSIONS

This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.

Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches

Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.

Rates of gene conversions between Escherichia coli ribosomal operons

Due to their universal presence and high sequence conservation, ribosomal RNA (rRNA) sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of rRNA genes to supply cells with sufficient capacity for protein synthesis. These copies typically undergo concerted evolution that keeps their sequences identical, or nearly so, due to gene conversion, a type of intragenomic recombination that changes one copy of a homologous sequence to exactly match another. Widely varying rates of rRNA gene conversion have previously been estimated by comparative genomics methods and using genetic reporter assays. To more directly measure rates of rRNA intragenomic recombination, we sequenced the seven Escherichia coli rRNA operons in 15 lineages that were evolved for ∼13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 38 gene conversion events and estimated an overall rate of intragenomic recombination within the 16S and 23S genes between rRNA copies of 3.6 × 10⁻⁴ per genome per generation or 8.6 × 10⁻⁶ per rRNA operon per homologous donor operon per generation. This rate varied only slightly from random expectations at different sites within the rRNA genes and between rRNA operons located at different positions in the genome. Our accurate estimate of the rate of rRNA gene conversions fills a gap in our quantitative understanding of how ribosomal sequences and other multicopy elements diversify and homogenize during microbial genome evolution.

Orthogonal translation enables heterologous ribosome engineering in E. coli

The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.

A spectrum of verticality across genes

Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, β-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners-an archaeal host, a mitochondrial symbiont, and a plastid ancestor-each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.

First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds

Background

Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner.

Methods

Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5-V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 × 2 contingency table tested for the independence between the 'number of AluI bands' and 'type of eletropherogram'.

Results

Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤5 or ≥6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity.

Conclusion

The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and -independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.

Contrasting diversity of vaginal lactobacilli among the females of Northeast India

BACKGROUND

Lactobacilli are gatekeepers of vaginal ecosystem impeding growth of pathogenic microbes and their diversity varies across populations worldwide. The present study investigated diversity of human vaginal microbiota among females of Northeast India, who are distinct in dietary habits, lifestyle, and genomic composition from rest of India.

RESULTS

Altogether, 154 bacterial isolates were obtained from vaginal swab samples of 40 pregnant and 29 non-pregnant females. The samples were sequenced for 16 s rRNA gene and analysed for identification using a dual approach of homology search and maximum likelihood based clustering. Molecular identification based on 16S rRNA gene sequence confirmed the isolates belonging to 31 species. Lactobacilli constituted 37.7% of the bacterial isolates with 10 species and other Lactic Acid Bacteria (39.61%) represented another 10 species, some of which are opportunistic pathogens. The remaining of the communities are mostly dominated by species of Staphylococcus (14.28%) and rarely by Propionibacterium avidum (3.90%), Bacillus subtilis, Escherchia coli, Janthinobacterium lividum, and Kocuria kristinae (each 0.64%). Interestingly Lactobacillus mucosae and Enterococcus faecalis, which are globally uncommon vaginal microbes is found dominant among women of Northeast India. This tentatively reflects adaptability of particular Lactobacillus species, in distinct population, to better compete for receptors and nutrients in vaginal epithelium than other species. Further, intrageneric 16S rRNA gene exchange was observed among Enterococcus, Staphylococcus, and two species of Lactobacillus, and deep intraspecies divergence among L. mucosae, which pinpointed possibility of emergence of new strains with evolved functionality. Lactobacilli percentage decreased from young pregnant to aged non-pregnant women with maximum colonization in trimester II.

CONCLUSION

The study highlighted importance of assessment of vaginal microbiota, Lactobacillus in particular, across different population to gain more insight on female health.

Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA

Bacterial species differ greatly in the number and location of the rRNA operons which may be present in the bacterial chromosomes and plasmids. Most bacterial species contain more than one ribosomal RNA operon copy in their genomes, with some species containing up to 15 such copies. We review the number and location of the rRNA operons and discuss evolution of 16S rRNA (rrs) genes -which are considered as ultimate chronometers for phylogenetic classification- in bacteria with multiple copies of these genes. In these bacterial species, the rrs genes must evolve in concert and sequence changes generated by mutation or horizontal gene transfer must be either erased or spread to every gene copy to avoid divergence, as it occurs when they are present in different species. Analysis of polymorphic sites in intra-genomic rrs copies identifies putative conversion events and demonstrates that sequence conversion is patchy and occurs in small conversion tracts. Sequence conversion probably arises by a non-reciprocal transfer between two or more copies where one copy contributes only a small contiguous segment of DNA, whereas the other copy contributes the rest of the genome in a fairly well understood molecular process. Because concerted evolution implies that a mutation in any of the rrs copies is either eliminated or transferred to every rrs gene in the genome, this process should slow their evolution rate relative to that of single copy genes. However, available data on the rrs genes in bacterial genomes do not show a clear relationship between their evolution rates and the number of their copies in the genome.

Testing culture purity in prokaryotes: criteria and challenges

Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer's personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by 'culturomics' will overcome this obstacle.

Phylogenetic Network Analysis Revealed the Occurrence of Horizontal Gene Transfer of 16S rRNA in the Genus Enterobacter

Horizontal gene transfer (HGT) is a ubiquitous genetic event in bacterial evolution, but it seldom occurs for genes involved in highly complex supramolecules (or biosystems), which consist of many gene products. The ribosome is one such supramolecule, but several bacteria harbor dissimilar and/or chimeric 16S rRNAs in their genomes, suggesting the occurrence of HGT of this gene. However, we know little about whether the genes actually experience HGT and, if so, the frequency of such a transfer. This is primarily because the methods currently employed for phylogenetic analysis (e.g., neighbor-joining, maximum likelihood, and maximum parsimony) of 16S rRNA genes assume point mutation-driven tree-shape evolution as an evolutionary model, which is intrinsically inappropriate to decipher the evolutionary history for genes driven by recombination. To address this issue, we applied a phylogenetic network analysis, which has been used previously for detection of genetic recombination in homologous alleles, to the 16S rRNA gene. We focused on the genus Enterobacter, whose phylogenetic relationships inferred by multi-locus sequence alignment analysis and 16S rRNA sequences are incompatible. All 10 complete genomic sequences were retrieved from the NCBI database, in which 71 16S rRNA genes were included. Neighbor-joining analysis demonstrated that the genes residing in the same genomes clustered, indicating the occurrence of intragenomic recombination. However, as suggested by the low bootstrap values, evolutionary relationships between the clusters were uncertain. We then applied phylogenetic network analysis to representative sequences from each cluster. We found three ancestral 16S rRNA groups; the others were likely created through recursive recombination between the ancestors and chimeric descendants. Despite the large sequence changes caused by the recombination events, the RNA secondary structures were conserved. Successive intergenomic and intragenomic recombination thus shaped the evolution of 16S rRNA genes in the genus Enterobacter.

Toxic genes present a unique phylogenetic signature

Horizontal gene transfer (HGT) is a major part of the evolution of Archaea and Bacteria, to the extent that the validity of the Tree of Life concept for prokaryotes has been seriously questioned. The patterns and routes of HGT remain a subject of intense study and debate. It was discovered that while several genes exhibit rampant HGT across the whole prokaryotic tree of life, others are lethal to certain organisms and therefore cannot be successfully transferred to them. We distinguish between these two classes of genes and show analytically that genes found to be toxic to a specific species (E. coli) also resist HGT in general. Several tools we employ show evidence to support that claim. One of those tools is the quartet plurality distribution (QPD), a mathematical tool that measures tendency to HGT over a large set of genes and species. When aggregated over a collection of genes, it can reveal important properties of this collection. We conclude that evidence of toxicity of certain genes to a wide variety of prokaryotes are revealed using the new tool of quartet plurality distribution.

A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species

A multilocus sequence analysis (MLSA) was established and performed on the genus Thioclava, including 23 strains isolated from diverse marine environments, with the aim of better differentiation of strains and species within this genus. The study was based on sequences of 16S rRNA gene and five protein-coding housekeeping genes, gyrB, rpoD, dnaK, trpB, and recA. In contrast to 16S rRNA gene-based tree that was unable to separate some species within this genus, each tree based on a single housekeeping gene and MLSA had consistently defined seven clades, corresponding to the five established ones and two novel ones. The digital DNA-DNA hybridization and average nucleotide identity analyses based on genome sequences of the representative strains reconfirmed the validity of the MLSA analysis, and recommended a 97.3% MLSA similarity as the soft species threshold and nine species representing the five known and four putative novel species. Two of the four new species were identified as Thioclava sediminum sp. nov. (type strain TAW-CT134^T = MCCC 1A10143^T = LMG 29615^T) and Thioclava marinus sp. nov. (type strain 11.10-0-13^T = MCCC 1A03502^T = LMG 29618^T) by using a polyphasic taxonomic approach. Taken together, the newly established MLSA in this study first described the variability and phylogeny of the genus Thioclava which contributes to better understanding its ecology and evolution.

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibrio strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANIb) and MUMmer (ANIm), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.

Molecular identification of Azospirillum spp.: Limitations of 16S rRNA and qualities of rpoD as genetic markers

Since their discovery, plant-growth promoting rhizobacteria from the genus Azospirillum have been subjected to intensive research due to their biotechnological potential as crop inoculants. Phylogenetic analysis of Azospirillum spp. is carried out by 16S rRNA sequencing almost exclusively, but inconsistencies and low confidence often arise when working with close species. In this work, it was observed that these difficulties might be explained by a high number of rRNA operons with considerable inter-genic variability within Azospirillum genomes. To search for alternative genetic markers from a list of housekeeping genes, the correlation between pairwise gene and whole-genome similarities was examined. Due to its good performance, rpoD was selected for further analyses. Genus-specific primers for the PCR-amplification and sequencing of rpoD from Azospirillum spp. were designed and tested on 16 type strains of different species. The sequences obtained were used for inferring a phylogenetic tree of the genus, which was in turn used as a reference to successfully identify a collection of 31 azospirilla isolated from many different locations of Argentine. In addition, several strains that might represent novel species were detected. The results indicate that the sequencing of rpoD is a suitable alternative method for a confident molecular identification in Azospirillum spp.

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

BACKGROUND

The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels.

RESULTS

In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that the percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage.

CONCLUSIONS

Our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases

Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.

Chlamydial Antibiotic Resistance and Treatment Failure in Veterinary and Human Medicine

The Chlamydiaceae are widespread pathogens of both humans and animals. Chlamydia trachomatis infection causes blinding trachoma and reproductive complications in humans. Chlamydia pneumoniae causes human respiratory tract infections and atypical pneumonia. Chlamydia suis infection is associated with conjunctivitis, diarrhea, and failure to gain weight in domestic swine. Chlamydial infections in humans and domesticated animals are generally controlled by antibiotic treatment—particularly macrolides (usually azithromycin) and tetracyclines (tetracycline and doxycycline). Tetracycline-containing feed has also been used to limit infections and promote growth in livestock populations, although its use has decreased because of growing concerns about antimicrobial resistance development. Because Sandoz and Rockey published an elegant review of chlamydial anti-microbial resistance in 2010, we will review the following: (i) antibiotic resistance in C. suis, (ii) recent evidence for acquired resistance in human chlamydial infections, and (iii) recent non-genetic mechanisms of antibiotic resistance that may contribute to treatment failure.

16S rRNA gene sequencing is a non-culture method of defining the specific bacterial etiology of ventilator-associated pneumonia

Ventilator-associated pneumonia (VAP) is an acquired respiratory tract infection following tracheal intubation. The most common hospital-acquired infection among patients with acute respiratory failure, VAP is associated with a mortality rate of 20-30%. The standard bacterial culture method for identifying the etiology of VAP is not specific, timely, or accurate in identifying the bacterial pathogens. This study used 16S rRNA gene metagenomic sequencing to identify and quantify the pathogenic bacteria in lower respiratory tract and oropharyngeal samples of 55 VAP patients. Sequencing of the 16S rRNA gene has served as a valuable tool in bacterial identification, particularly when other biochemical, molecular, or phenotypic identification techniques fail. In this study, 16S rRNA gene sequencing was performed in parallel with the standard bacterial culture method to identify and quantify bacteria present in the collected patient samples. Sequence analysis showed the colonization of multidrug-resistant strains in VAP secretions. Further, this method identified Prevotella, Proteus, Aquabacter, and Sphingomonas bacterial genera that were not detected by the standard bacterial culture method. Seven categories of bacteria, Streptococcus, Neisseria, Corynebacterium, Acinetobacter, Staphylococcus, Pseudomonas and Klebsiella, were detectable by both 16S rRNA gene sequencing and standard bacterial culture methods. Further, 16S rRNA gene sequencing had a significantly higher sensitivity in detecting Streptococcus and Pseudomonas when compared to standard bacterial culture. Together, these data present 16S rRNA gene sequencing as a novel VAP diagnosis tool that will further enable pathogen-specific treatment of VAP.