Updating the 97% identity threshold for 16S ribosomal RNA OTUs

Screening a 681-membered yeast collection for the secretion of proteins with antifungal activity

Fungal pathogens pose a threat to human health and food security. Few antifungals are available and resistance to all has been reported. Novel strategies to control plant and human pathogens as well as food spoilers are urgently required. Environmental yeasts provide a functionally diverse, yet underexploited potential for fungal control based on their natural competition via the secretion of proteins and other small molecules such as iron chelators, volatile organic compounds or biosurfactants. However, there is a lack of standardized workflows to systematically access application-relevant yeast-based compounds and understand their molecular functioning. Towards this goal, we developed a workflow to identify and characterize yeast isolates that are active against spoilage yeasts and relevant human and plant pathogens, herein focusing on discovering yeasts that secrete antifungal proteins. The workflow includes the classification of the secreted molecules and cross-comparison of their antifungal capacity using an independent synthetic calibrant. Our workflow delivered a collection of 681 yeasts of which 212 isolates (31 %) displayed antagonism against at least one target strain. While 57.5 % of the active yeasts showed iron-depended antagonism, likely due to pulcherrimin-like iron chelators, 31.7 % secreted antifungal proteins. Those yeast candidates clustered within twelve OTUs, showed narrow and broad target spectra, and several showed a broad pH and temperature activity profile. Given the tools for yeast biotechnology and protein engineering available, our collection can serve as a rich starting point for genetic and molecular characterization of the various antifungal phenotypes, their mode of action and their future exploitation.

Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities

Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.

Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing

Insect gut microbiota play important roles in host health and interactions with the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, such as the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to establish in hosts is important for the establishment of lost or novel microbiota in mass-reared insects. The goal of this study was to evaluate how host age and diet-inoculation method influenced bacterial establishment in laboratory and mass-reared medflies. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio Kinnex 16S rRNA sequencing to track the establishment of the specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. The target bacterial isolate was detected in medfly when inoculated with liquid diet regardless of age, but those fed a slurry-based diet and a separate water source had less establishment. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.

IMPORTANCE

Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goal of our study was to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species worldwide. Mass-reared insects for the sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medflies. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

Rare and Intermediate Taxa Shape the Gut Bacterial Structure in Neonates and Preterm Infants with Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is a common neonatal gastrointestinal disease with high morbidity and mortality, especially in premature infants. In a prospective case-control study, we aimed to investigate the dynamic changes in the gut microbiota of preterm infants with NEC. Infants diagnosed with NEC and preterm neonates were enrolled in this study, while normal neonates were selected as the control group. The collected samples were divided into three groups: the control group (NC), the neonatal NEC group (NEC), and the premature delivery NEC group (pdNEC). Along with basic clinical data, fecal samples from the infants (n = 39) were collected at the time of the first diagnosis of NEC for 16S rRNA gene sequencing. Analysis of the gut microbiota revealed no significant difference in α-diversity between infants with NEC and controls, regardless of preterm birth. The significant difference in β-diversity was primarily driven by the rare and intermediate subgroups. The rare gut subgroup found in premature infants with NEC played a crucial role in the deterministic process and specialized functionality of the microbiota, ultimately forming a sparse association network structure. Finally, multiple biomarkers of Enterococcus from the Firmicutes phylum were identified, providing a theoretical basis for diagnosing NEC in premature infants.

The unresolved struggle of 16S rRNA amplicon sequencing: a benchmarking analysis of clustering and denoising methods

BACKGROUND

Although 16S rRNA gene amplicon sequencing has become an indispensable method for microbiome studies, this analysis is not error-free, and remains prone to several biases and errors. Numerous algorithms have been developed to eliminate these errors and consolidate the output into distance-based Operational Taxonomic Units (OTUs) or denoising-based Amplicon Sequence Variants (ASVs). An objective comparison between them has been obscured by various experimental setups and parameters. In the present study, we conducted a comprehensive benchmarking analysis of the error rates, microbial composition, over-merging/over-splitting of reference sequences, and diversity analyses using the most complex mock community, comprising 227 bacterial strains and the Mockrobiota database. Using unified preprocessing steps, we were able to compare DADA2, Deblur, MED, UNOISE3, UPARSE, DGC (Distance-based Greedy Clustering), AN (Average Neighborhood), and Opticlust objectively.

RESULTS

ASV algorithms-led by DADA2- resulted in having a consistent output, yet suffered from over-splitting, while OTU algorithms-led by UPARSE-achieved clusters with lower errors, yet with more over-merging. Notably, UPARSE and DADA2 showed the closest resemblance to the intended microbial community, especially when considering measures for alpha and beta diversity.

CONCLUSION

Our unbiased comparative evaluation examined the performance of eight algorithms dedicated to the analysis of 16S rRNA amplicon sequences with a wide range of mock datasets. Our analysis shed light on the pros and cons of each algorithm and the accuracy of the produced OTUs or ASVs. The utilization of the most complex mock community and the benchmarking comparison presented here offer a framework for the comparison between OTU/ASV algorithms and an objective method for the assessment of new tools and algorithms.

Cyanobacterium Nostoc species mitigate soybean cyst nematode infection on soybean by shaping rhizosphere microbiota

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating and yield-limiting pathogen that threatens soybean production globally. Sustainable SCN disease management strategies are needed. In this study, a cyanobacterial strain was isolated from SCN-infected soybean soil and identified as Nostoc punctiforme using the cyanobacterial 16S rRNA gene sequence. When susceptible soybean plants were grown in the SCN-inoculated soil, N. punctiforme inoculants significantly reduced the total number of SCN eggs and second-stage juveniles (J2s), compared to the control with SCN inoculation only. Further microbial analysis showed that N. punctiforme inoculants changed the bacterial and fungal communities in the soybean rhizospheres and significantly increased the relative abundance of several bacterial and fungal species with potential nematicidal activities, suggesting the changes of soybean rhizosphere microbiota may partially contribute to the activity of N. punctiforme inoculants against SCN. However, N. punctiforme inoculants did not directly induce soybean defense reactions against SCN. Thus, N. punctiforme may be a potential microbial source against SCN invasion in soybean.

Nitrous oxide emissions treating hypersaline wastewater in suspended and attached partial nitritation - anammox reactors

Nitrous oxide (N2O) emissions from partial nitritation- anammox (PN/A) processes for deammonification has become an important issue as the technology has become more widespread, however, N2O emissions from PN/A treating hypersaline wastewater has been little reported. Here, N2O emissions from completely mixed suspended and attached single-stage PN/A reactors treating hypersaline (4 % salinity; 40 g/kg) wastewater for ammonium removal were first investigated without the addition of organics. Results show that N2O emissions in fixed bed and suspended PN/A reactors without organic addition ranged from 0.08 % to 1.0 % and 0.09 % to 1.5 % of ammonium removed, respectively. Bulk ammonium and nitrite concentrations were shown to be the main controlling factors for N2O emissions. The presence of influent organics was subsequently studied to see its effect on nitrogen removal and N2O emissions. The addition of acetate to both fixed bed and suspended reactors reduced N2O emissions by 52.5 % and 72.4 %, respectively. Quantitative PCR results showed an increase in the functional genes related to denitrification with the addition of acetate, however, deammoniafication was not significantly affected.

Green land in a landscape bolsters the dietary diversity of reared yellow-legged hornet Vespa velutina Lepeletier (Hymenoptera: Vespidae)

Land use change has significantly altered most ecosystem functioning, such as nutrition provisioning, water flows and pollination services. So far, the impact of land use change on the dietary diversity of predatory insects has remained largely unexplored. In this study, we explored the prey composition of reared yellow-legged hornets Vespa velutina Lepeletier (Hymenoptera: Vespidae) in landscapes with a gradient of surrounding green lands, using metabarcoding of feces eliminated by larvae. The hornets primarily fed upon insects, with dipterans, coleopterans, lepidopterans, hemipterans, hymenopterans, and orthopterans being the dominant prey groups. The percentage of green lands had a significantly positive effect on prey richness at a spatial scale of 1500 m, but no effect on Shannnon index of the prey community. Meanwhile, the green lands had significantly positive effects on richness of coleopteran prey and lepidopteran prey, but no significant effect on richness of dipteran prey, hemipteran prey, hymenopteran prey, or orthopteran prey. In terms of beta diversity, the percentage of green lands explained the dissimilarity of prey communities among landscapes, whereas local factors, such as the distance to green lands and the distance to buildings, did not explain the dissimilarity. Our study indicated that the green lands in the landscape positively affected the dietary diversity of reared yellow-legged hornets, but this effect varied among different taxonomic groups of prey.

Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury

BACKGROUND

Recent studies have highlighted the potential influence of gut dysbiosis on traumatic brain injury (TBI) outcomes. Alterations in the abundance and diversity of Lactobacillus species may affect immune dysregulation, neuroinflammatory responses, anxiety- and depressive-like behaviors, and neuroprotective mechanisms activated in response to TBI.

OBJECTIVE

This study aims to evaluate the protective and preventive effects of Pan-probiotic (PP) treatment on the inflammatory response during both the acute and chronic phases of TBI.

METHODS

Males and female mice underwent controlled cortical impact (CCI) injury or sham. They received a PP mixture in drinking water containing strains of Lactobacillus plantarum, L. reuteri, L. helveticas, L. fermentum, L. rhamnosus, L. gasseri, and L. casei. In the acute group, mice received PP or vehicle (VH) treatment for 7 weeks before TBI, continuing until 3 days post-injury (dpi). In the chronic group, treatment began 2 weeks before TBI and was extended through 35 dpi. The taxonomic microbiome profiles of fecal samples were evaluated using 16S rRNA V1-V3 sequencing analysis, and Short-chain fatty acids (SCFAs) were measured. Immunohistochemical, in situ hybridization, and histological analyses were performed to assess neuroinflammation post-TBI, while behavioral assessments were conducted to evaluate sensorimotor and cognitive functions.

RESULTS

Our findings suggest that a 7-week PP administration induces specific microbial changes, including increased abundance of beneficial bacteria such as Lactobacillaceae, Limosilactobacillus, and Lactiplantibacillus. PP treatment reduces lesion volume and cell death at 3 dpi, elevates SCFA levels at 35 dpi, and decreases microglial activation at both time points, particularly in males. Additionally, PP treatment improved motor recovery in males and alleviated depressive-like behaviors in females.

CONCLUSION

Our findings indicate that PP administration modulates microbiome composition, reduces neuroinflammation, and improves motor deficits following TBI, with these effects being particularly pronounced in male mice.

A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies

Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.

Exploring methanogenic archaea and their thermal responses in the glacier-fed stream sediments of Rongbuk River basin, Mt. Everest

Glacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mt. Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5°C and 15°C. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and hydrogen-dependent methylotrophic types. Substantial methane and CO2 production were detected across altitudes and increased significantly at 15°C, with both methane and CO2 production rates negatively correlated with altitude. The temperature sensitivity of CO2 production also showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15°C, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed for Methanomassiliicoccaceae and Methanoregulaceae, and negative correlations for Methanocellaceae, respectively. Besides altitude, phosphorus, carbon to nitrogen ratio, and pH also affected methanogenic structure, methane and CO2 production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.

Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy

The 16S rRNA gene is frequently sequenced to classify prokaryotes and identify new taxa. If sequences from two strains share less than ~99% identity, the strains are usually classified as different species. Classification thresholds for genera and other ranks have also been proposed, but they are based on dated datasets. Here we update these thresholds by determining the sequence identity of the 16S rRNA gene for n=19,556 type strains. This represents 94% of all strains validly published, and it involved making more than 191 million pairwise sequence alignments. In 90% of all cases, sequences from the same species shared a minimum of 97.2-100% identity. The corresponding values were 90.1-99.0% for genus, 80.1-94.1% for family, 72.9-90.0% for order, 72.2-86.3% for class and 69.6-83.6% for phylum. We also present values specific to bacteria (n=18,904 strains) and archaea (n=652 strains). We propose these values serve as thresholds for classifying new prokaryotic taxa. A major change from previous guidelines is recognizing that these boundaries overlap. This overlap has already been observed for relative evolutionary divergence, a metric correlated with 16S rRNA gene identity. Together with other metrics, 16S rRNA gene identity allows classification of prokaryotes from species to phylum.

Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database

Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.

Opposite effects of N on warming-induced changes in bacterial and fungal diversity

The diversity of bacteria and fungi is linked to distinct ecosystem functions, and divergent responses to global changes in these two kingdoms affect the relative contributions of the kingdoms to the soil carbon and nutrient cycles. Climate warming and nitrogen (N) enrichment, which are projected to increase concurrently through modelling efforts, are considered the main drivers of biodiversity loss. However, it is unclear how bacterial and fungal diversity respond differently to the simultaneous occurrence of climate warming and nitrogen enrichment, and the underlying mechanisms involved remain unknown. Using a 9-yr warming and N enrichment experiment in an alpine permafrost area of the Tibetan Plateau, we demonstrated the contrasting response of bacterial and fungal diversity to combined warming and N enrichment, showing a reduction in bacterial richness (8.8%) and an increase in fungal diversity (33.6%). Furthermore, the negative effects of warming on fungal richness were reversed by N enrichment, and the negative effects of nitrogen enrichment on bacteria were amplified by warming. Our results also demonstrated that both biotic interactions, such as bacterial-fungal antagonism, and abiotic factors, primarily the soil C/N ratio and pH, play crucial roles in shaping microbial biodiversity. Our findings suggest that fungal diversity is expected to greatly increase in a warmer and more nitrogen-enriched world, potentially leading to the enhancement of ecosystem functions driven by fungi.

Short-read next-generation sequencing of 16s rRNA gene amplicons for characterizing amplicon sequence variants (ASVs) and determination of gene copy numbers using ion Torrent platform

The short-amplicon sequencing of hypervariable regions of 16S rRNA gene is the widely used method for bacterial identification and microbiota profiling. Bacteria possess multiple copies of 16S rRNA gene and may contain single nucleotide variations (SNPs) or amplicon sequence variants (ASVs). The ASVs based determination of microbial taxa can be better representation over operational taxonomic units (OTUs). Illumina based NGS platforms are mostly used to define the ASVs whereas Ion-torrent platform is commonly used for diagnostic purposes. We aimed to identify bacterial isolates having ASVs and infer the copy numbers of16S rRNA gene using short read sequencing performed on the Ion Gene Studio S5 NGS platform. The V2-V3 regions of 16S rRNA gene were amplified from the bacterial isolates and subjected to NGS. Further, the sequences produced by NGS were compared with those generated from Sanger sequencing. The bacterial isolates were identified and characterize during ASVs. The copy number of the 16S rRNA gene was established in Gram-negative isolates. Assigning bacterial taxa based on ASVs would provide a more accurate representation of the variant data.

Nanopore Sequencing of Amoebophrya Species Reveals Novel Collection of Bacteria Putatively Associated With Karlodinium veneficum

The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate K. veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole-genome sequencing of an Amoebophrya sp. ex K. veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, 13 were identifiable at the generic level by BLAST (8 of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for <2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of metagenome-assembled genomes are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.

Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles

Bacteroides species are key members of the human gut microbiome and play crucial roles in gut ecology, metabolism, and host-microbe interactions. This study investigated the strain-specific production of neuroactive metabolites by 18 Bacteroidetes (12 Bacteroides, 4 Phocaeicola, and 2 Parabacteroides) using multi-omics approaches. Genomic analysis revealed a significant potential for producing GABA, tryptophan, tyrosine, and histidine metabolism-linked neuroactive compounds. Using untargeted and targeted metabolomics, we identified key neurotransmitter-related or precursor metabolites, including GABA, l-tryptophan, 5-HTP, normelatonin, kynurenic acid, l-tyrosine, and norepinephrine, in a strain- and media-specific manner, with GABA (1-2 mM) being the most abundant. Additionally, extracellular vesicles (EVs) produced by Bacteroides harbor multiple neuroactive metabolites, mainly GABA, and related key enzymes. We used CRISPR/Cas12a-based gene engineering to create a knockout mutant lacking the glutamate decarboxylase gene (gadB) to demonstrate the specific contribution of Bacteroides finegoldii-derived GABA in modulating intestinal homeostasis. Cell-free supernatants from wild-type (WT, GABA+) and ΔgadB (GABA-) provided GABA-independent reinforcement of epithelial membrane integrity in LPS-treated Caco-2/HT29-MTX co-cultures. EVs from WT and ΔgadB attenuated inflammatory immune response of LPS-treated RAW264.7 macrophages, with reduced pro-inflammatory cytokines (IL-1β and IL-6), downregulation of TNF-α, and upregulation of IL-10 and TGF-β. GABA production by B. finegoldii had a limited impact on gut barrier integrity but a significant role in modulating inflammation. This study is the first to demonstrate the presence of a myriad of neuroactive metabolites produced by Bacteroides species in a strain- and media-specific manner in supernatant and EVs, with GABA being the most dominant metabolite and influencing immune responses.

Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. However, their involvement in the gut-brain axis has been poorly investigated. We hypothesize that MEVs cross host cellular barriers and deliver their cargoes of bioactive compounds to the brain. In this study, we aimed to investigate the cargo capacity of MEVs for bioactive metabolites and their interactions with the host cellular barriers. First, we conducted a multi-omics profiling of MEVs' contents from ex vivo and stool samples. Metabolomics analysis identified various neuro-related compounds encapsulated within MEVs, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines. Metaproteomics unveiled an enrichment of enzymes involved in neuronal metabolism, primarily in the glutamine/glutamate/gamma-aminobutyric acid (GABA) pathway. These neuro-related proteins and metabolites were correlated with Bacteroides spp. We isolated 18 Bacteroides strains and assessed their GABA production capacity in extracellular vesicles (EVs) and culture supernatant. A GABA-producing Bacteroides finegoldii, released EVs with a high GABA content (4 µM) compared to Phocaeicola massiliensis. Upon testing the capacity of MEVs to cross host barriers, MEVs exhibited a dose-dependent paracellular transport and were endocytosed by Caco-2 and hCMEC/D3 cells. Exposure of Caco-2 cells to MEVs did not alter expression of genes related to intestinal barrier integrity, while affected immune pathways and cell apoptosis process as revealed by RNA-seq analyses. In vivo, MEVs biodistributed across mice organs, including the brain, liver, stomach, and spleen. Our results highlight the ability of MEVs to cross the intestinal and blood-brain barriers to deliver their cargoes to distant organs, with potential implication for the gut-brain axis.

IMPORTANCE

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. In this study, a multi-level analysis revealed presence of a diverse array of biologically active molecules encapsulated within MEVs, including neuroactive metabolites, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines, and gamma-aminobutyric acid (GABA). Metaproteomics also unveiled an enrichment of neural-related proteins, mainly the glutamine/glutamate/GABA pathway. MEVs were able to cross epithelial and blood-brain barriers in vitro. RNA-seq analyses showed that MEVs stimulate several immune pathways while suppressing cell apoptosis process. Furthermore, MEVs were able to traverse the intestinal barriers and reach distal organs, including the brain, thereby potentially influencing brain functionality and contributing to mental and behavior.

Facade eluates affect active and total soil microbiome

The application of biocides in building materials has become a prevalent practice to mitigate the growth of microorganisms such as algae, fungi, and bacteria on the façades. These can leach out from the material and reach the nearby soil environment. This study aimed to characterize the effect of façade eluates generated within different leaching experiments on total and metabolic active soil microbial community composition and functions. Façade eluates were produced by immersion testing DIN EN 16105 and a natural weathering experiment. Afterward, soil microcosms were treated with the respective façade eluate and incubated for 29 days. Subsequently, the active and total soil microbial community compositions were investigated. Fungal internal transcribed spacer region gene and bacterial 16S rRNA gene were sequenced for active (bromodeoxyuridine labeled DNA) microbial community and total community. Façade eluates reduced total bacterial and fungal gene copy numbers. Overall, active bacterial and fungal richness was reduced and altered in community composition in comparison to the total richness and composition, respectively. Façade eluates retrieved of façade samples without biocides did alter the soil microbial communities to the same extent as façade eluates with biocides. Additionally, members of the active microbiome that benefit from the presence of façade eluates and omitted ones could be identified. Our result demonstrated that façade eluates affect active and total soil microbial community composition and function regardless of the leaching procedure and biocides addition.

Corynebacterium mayonis sp. nov. isolated from a human blood culture

A novel Corynebacterium species, strain BD556T, isolated from blood, was identified at Mayo Clinic, Rochester, MN, USA. After failing definitive identification using MALDI-ToF MS and partial 16S rRNA gene sequencing, BD556T was characterized using a polyphasic approach, including phenotypic, biochemical and whole-genome sequencing methods. BD556T was a Gram-positive rod with clubbed ends, facultatively anaerobic, catalase-positive, oxidase-negative and non-motile. Colonies were white, opaque and non-haemolytic with halo-like edges. BD556T grew at 35 °C in room air, with CO2 and under anaerobic conditions. BD556T grew well in 0 and 6% NaCl and weakly in 10% NaCl. The genome size was 2 349 779 bp with a G+C content of 60.39%. Phylogenetic analysis using 16S rRNA gene sequence analysis, average nucleotide identity and digital DNA-DNA hybridization between the genome of BD556T and the closest type strains from the Type Strain Genome Server database yielded separation values well beyond those required for species delineation. Chemotaxonomic analyses of BD556T revealed ribose, arabinose and galactose as whole-cell sugars and an A1γ meso-diaminopimelic acid-direct peptidoglycan type. The major cellular fatty acids were C15 : 0 (21.0%), C16 : 0 (14.8%), C17 : 1 ω9c (26.2%), C17 : 0 (13.3%) and C18 : 1 ω9c (18.3%). Polar lipids included diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids and phospholipids. BD556T also contained mycolic acids (32-36 carbons) typical of corynebacteria. The respiratory quinones were dominated by MK-8(H2) (71.2%) and MK-9(H2) (25.9%), with smaller amounts of MK-7(H2) and MK-10(H2). The results presented support the tenet that BD556T (=TSD 427T=NCTC 15078T) is a novel species for which the name Corynebacterium mayonis sp. nov. is proposed.

Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes

The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.

The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children

Respiratory syncytial virus (RSV) is the leading cause of infant respiratory infections and hospitalizations. To investigate the relationship between the respiratory microbiome and RSV infection, we sequence nasopharyngeal samples from a birth cohort and a pediatric case-control study (Respiratory Syncytial virus Consortium in Europe [RESCEU]). 1,537 samples are collected shortly after birth ("baseline"), during RSV infection and convalescence, and from healthy controls. We find a modest association between baseline microbiota and the severity of consecutive RSV infections. The respiratory microbiota during infection clearly differs between infants with RSV and controls. Haemophilus, Streptococcus, and Moraxella abundance are associated with severe disease and persistence of symptoms, whereas stepwise increasing abundance of Dolosigranulum and Corynebacterium is associated with milder disease and health. We conclude that the neonatal respiratory microbiota is only modestly associated with RSV severity during the first year of life. However, the respiratory microbiota at the time of infection is strongly associated with disease severity and residual symptoms.

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data

BACKGROUND

Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.

RESULTS

Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n = 18), while DADA2 results for the same replicates were highly heterogeneous.

CONCLUSIONS

Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.

Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques

Rhesus cytomegalovirus expressing simian immunodeficiency virus (RhCMV/SIV) vaccines protect ~59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is unknown. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here, we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection. Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post-challenge and were profiled using 16S rRNA based microbiome analysis. We identified ~2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, by using newly developed compositional data analysis techniques, we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.IMPORTANCEThe human immunodeficiency virus (HIV) has infected millions of people worldwide. Unfortunately, still there is no vaccine that can prevent or treat HIV infection. A promising pre-clinical HIV vaccine based on rhesus cytomegalovirus (RhCMV) expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) provides sustained, durable protection against SIV challenge in ~59% of vaccinated rhesus macaques. There is an urgent need to understand the cause of this protection vs non-protection outcome. In this study, we profiled the gut microbiomes of 45 RhCMV/SIV vaccinated rhesus macaques and identified gut microbial signatures that were predictive of RhCMV/SIV vaccination groups and vaccine protection outcomes. These vaccine protection-associated microbial features were significantly correlated with early vaccine-induced host immune signatures in whole blood from the same animals. These findings show that the gut microbiome may be involved in RhCMV/SIV vaccine-induced protection, warranting further research into the impact of the gut microbiome in human vaccine trials.

Comprehensive genomic analysis and evaluation of in vivo and in vitro safety of Heyndrickxia coagulans BC99

This study aimed to evaluate the safety profile and beneficial effects of Heyndrickxia coagulans strain BC99 (BC99) for potential use in functional foods and pharmaceuticals. We began with whole genome sequencing of BC99, followed by a comprehensive safety assessment comprising genome analysis, hemolysis, cytotoxicity, antibiotic susceptibility tests, and cell adhesion and tolerance studies, along with acute and subacute oral toxicity studies in animal models. BC99 was isolated from a well-characterized collection originating from the feces of a healthy infant. Our results indicated no hemolytic activity on Columbia blood agar plates and broad antibiotic sensitivity, including to gentamicin, ampicillin, chloramphenicol, ciprofloxacin, and others. Cytotoxicity testing confirmed no adverse effects on HT-29 cells and significant adhesive properties to intestinal epithelial cells. Tolerance tests demonstrated over 90% viability of BC99 under simulated gastrointestinal conditions. In vivo studies in mice and rats confirmed the absence of adverse effects following oral administration. Collectively, these findings support BC99's robust tolerance to gastrointestinal environments, strong adhesion capabilities, and a broad spectrum of antibiotic resistance, underlining its potential as a safe and effective agent for gut microbiota modulation and host health enhancement.

Chronic osteoarthritis caused by Propionibacterium australiense infection in a captive sand gazelle

Osteoarthritis is a common cause of morbidity and mortality in geriatric gazelles. Propionibacterium australiense has been reported as a cause of systemic granulomas in cattle, but there are no descriptions of this bacteria infecting other species nor causing osteoarthritis, to our knowledge. An 8-y-old, castrated male, sand gazelle (Gazella leptoceros leptoceros) was managed for chronic, intermittent, progressive osteoarthritis of the right tarsus. Serial biopsies revealed pyogranulomatous dermatitis with intralesional bacteria. Serial diagnostic imaging identified osseous and soft tissue proliferation with draining tracts. Treatments over 1 y included broad-spectrum antibiotics, anti-inflammatories, joint debridement, and infusion with platelet-rich plasma and stem cells. Despite therapy, lameness persisted, azotemia developed, and subsequently, the animal was euthanized. On postmortem examination, the periarticular tissue of the right tarsus was markedly expanded by pyogranulomas and fibrosis. Histologically, the synovium, joint capsule, and overlying soft tissues were markedly expanded by pyogranulomas and numerous gram-positive and acid-fast-negative filamentous bacteria surrounded by Splendore-Hoeppli material. Within the joint, there was regionally extensive cartilage ulceration, osteonecrosis, osteolysis, and pannus formation. PCR assay of affected formalin-fixed, paraffin-embedded tissue amplified segments of 16S rRNA and β subunit of bacterial RNA polymerase (rpoB) genes with 99.7% and 95.6% identity to P. australiense. This bacterium should be considered a differential for chronic pyogranulomatous osteoarthritis in gazelles.

Emergence of highly virulent and multidrug-resistant Escherichia coli in breeding sheep with pneumonia, Hainan Province, China

Background

Sheep are a rarely raised livestock in Hainan Island, China, because of the unfavorable tropical marine climate. Here, this article reports a severe pneumonia in the sheep breeding and domestication facility caused acute mortality during the winter 2021-2022.

Methods

Six sheep were clinically dissected and histopathologically observed. The bacteria were isolated and cultured by traditional methods and identified by 16S rRNA sequencing. The genotypes, serotypes, virulence genes and antimicrobial resistance genes were analyzed by PCR and whole genome sequencing. The pubMLST website was used for phylogenetic analysis of related strains. Kirby-Bauer disk diffusion method was used for antimicrobial susceptibility test. The antimicrobial susceptibility test standard was referred to the Clinical and Laboratory Standards Institute (CLSI). The virulence of bacteria was detected by mouse infection model.

Results

Etiology and histopathology examination of the pneumonia reveled pulmonary abscess and alveolar neutrophilia and pulmonary fibrinous exudates. Escherichia coli was the only bacterial species isolated, primarily from the lungs and blood of the six dead or moribund sheep, a total of 29 E. coli strains were isolated. Antimicrobial resistance profiling shows that all the isolates were resistant to six agents (penicillin, ampicillin, cephalothin, neomycin, erythromycin, and vancomycin) belonging to five classes of antibiotics, classifying them as multi drug resistant (MDR). Furthermore, genotyping analysis revealed all strains were common with 11-17 virulence factors indicating high pathogenicity. The lab mice infection model shows that all strains severely affect the health status particularly weight loss, lethargy, pneumonia and shortly lead to death. The molecular epidemiological analysis indicated most strains share the same genotype as previously reported strains in humans and other farmed animals this suggests a high possibility of cross-species transmission (CST) of virulent and MDR isolates. This CST could be from sheep to humans and other farmed animals or from humans and other farmed animals to sheep.

Conclusion

Therefore, this study indicates that E. coli is an emerging threat that causes sheep pneumonia in Hainan, and the quarantine of contacts is important to control the spread of virulent E. coli and the transmission of acquired resistance genes between humans and farmed animals such as sheep.

Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria

The low cultivability of environmental bacteria has been widely acknowledged, but most previous estimates focused on the proportion of cultivable cells rather than cultivable taxa. Here, we estimate the proportions of cultivable cells and cultivable taxa for two sample types (soil and activated sludge) using cell counting, 16S rRNA gene amplicon sequencing, metagenomics, and cultivation on agar plates under various conditions. We find that the proportion of cultivable taxa exceeds that of cultivable cells at the sample level. A large proportion of cultivable taxa are taxonomically novel but tend to be present at very low abundance on agar plates, forming microcolonies, and some of them cease to grow during subculture. Compared with uncultivable taxa (under the conditions used in our study), cultivatable taxa tend to display higher metabolic activity as inferred by measuring rRNA copies per cell. Finally, we use the generated taxonomic and genomic information as a guide to isolate a strain representing a yet-uncultured class within the Bacteroidota and to enhance the cultivable diversity of Burkholderiales from activated sludge.

Temperature, sediment resuspension, and salinity drive the prevalence of Vibrio vulnificus in the coastal Baltic Sea

The number of Vibrio-related infections in humans, e.g., by Vibrio vulnificus, has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic Vibrio spp., like V. vulnificus. To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of Vibrio spp. and V. vulnificus in water were compared to environmental conditions, including the presence of the eelgrass Zostera marina, which has been suggested to reduce pathogenic Vibrio species abundance. In the water column, V. vulnificus only occurred at the German station between July and August at salinity 8.1-11.2. Temperature and phosphate (PO43-) were identified as the most influencing factors for Vibrio spp. and V. vulnificus. The accumulation of Vibrio spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to V. vulnificus abundance. Interestingly, V. vulnificus co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in Vibrio spp. or V. vulnificus associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO43-, for Vibrio species levels at intermediate salinities in the Baltic Sea.

IMPORTANCE

Elevated sea surface temperatures are increasing the prevalence of pathogenic Vibrio at higher latitudes. The recent increase in Vibrio-related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on Vibrio vulnificus, and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of V. vulnificus at intermediate salinities in the coastal Baltic Sea.

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs

BACKGROUND

Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read.

RESULTS

Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3-40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes.

CONCLUSION

PenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities. Video Abstract.

Analysis of genomic and characterization features of Luteolibacter soli sp. nov., isolated from soil

The strain designated as Y139T is a novel Gram-stain-negative, aerobic, and non-motile bacterium, was isolated from a soil sample in McClain County, Oklahoma, United States. The cells of strain Y139T were a rod-shaped, with the width of 0.4-0.7 μm and the length of 1.5-2.0 μm . Growth occurred at 20-37°C (optimum, 30°C), pH 5.5-9.5 (optimum, pH 7.0), and 0-1.0% NaCl (w/v) (optimum, 0%). The polar lipid profiles included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, and an unidentified lipid. The major fatty acids included C16:0, iso-C14:0, and C16:1 ω9c. Menaquinone-9 (MK-9) was recognized as the only respiratory quinone. Strain Y139T showed the highest 16S rRNA gene sequence similarity to Luteolibacter flavescens MCCC 1K03193T (98.3%). Phylogenetic analysis positioned it within the genus Luteolibacter. The draft genome of strain Y139T consisted of 7,106,054 bp, and contained 5,715 open reading frames (ORFs), including 5,656 coding sequences (CDSs) and 59 RNA genes. The genomic DNA G + C content was found to be 62.5%. Comparing strain Y139T with L. flavescens MCCC 1K03193T and Luteolibacter arcticus CCTCC AB 2014275T, the average nucleotide identity (ANI) values were 80.6 and 82.1%, respectively. Following phylogenetic, physiological, biochemical, and chemotaxonomic analyses, a novel species within the genus Luteolibacter, designated as Luteolibacter soli sp. nov., was proposed for strain Y139T, which was also assigned as the type strain (=KCTC 92644T = MCCC 1H01451T). Further analysis of core genes across 9 Luteolibacter species uncovered significant genomic divergence, particularly in those related to cofactor, vitamin, and energy metabolism. Analysis of biogeographic distribution suggested that lake and soil were the main habitats for the genus Luteolibacter. Additionally, the genus Luteolibacter was sensitive to climate warming and precipitation.

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces

Streptomyces is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of Streptomyces would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based Streptomyces classifications using 2276 publicly available Streptomyces genome assemblies and 48 981 publicly available full-length 16S rRNA Streptomyces sequences from silva, Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14 239 distinct Streptomyces sequences that resolves three major lineages of Streptomyces, but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for Streptomyces, demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate Streptomyces species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as Streptomyces taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the Streptomyces community.

Integrative Analysis of Probiotic-Mediated Remodeling in Canine Gut Microbiota and Metabolites Using a Fermenter for an Intestinal Microbiota Model

In contemporary society, the increasing number of pet-owning households has significantly heightened interest in companion animal health, expanding the probiotics market aimed at enhancing pet well-being. Consequently, research into the gut microbiota of companion animals has gained momentum, however, ethical and societal challenges associated with experiments on intelligent and pain-sensitive animals necessitate alternative research methodologies to reduce reliance on live animal testing. To address this need, the Fermenter for Intestinal Microbiota Model (FIMM) is being investigated as an in vitro tool designed to replicate gastrointestinal conditions of living animals, offering a means to study gut microbiota while minimizing animal experimentation. The FIMM system explored interactions between intestinal microbiota and probiotics within a simulated gut environment. Two strains of commercial probiotic bacteria, Enterococcus faecium IDCC 2102 and Bifidobacterium lactis IDCC 4301, along with a newly isolated strain from domestic dogs, Lactobacillus acidophilus SLAM AK001, were introduced into the FIMM system with gut microbiota from a beagle model. Findings highlight the system's capacity to mirror and modulate the gut environment, evidenced by an increase in beneficial bacteria like Lactobacillus and Faecalibacterium and a decrease in the pathogen Clostridium. The study also verified the system's ability to facilitate accurate interactions between probiotics and commensal bacteria, demonstrated by the production of short-chain fatty acids and bacterial metabolites, including amino acids and gamma-aminobutyric acid precursors. Thus, the results advocate for FIMM as an in vitro system that authentically simulates the intestinal environment, presenting a viable alternative for examining gut microbiota and metabolites in companion animals.

Reproducible chemostat cultures to minimize eukaryotic viruses from fecal transplant material

Recent studies indicate an important role of bacteriophages for successful fecal microbiota transplantation (FMT). However, wider clinical applications of FMT are hampered by to donor variability and concerns of infection risks by bacteria and human viruses. To overcome these challenges, mouse cecal and human fecal material were propagated in a chemostat fermentation setup supporting multiplication of bacteria, and phages, while propagation of eukaryotic viruses will be prevented in the absence of eukaryotic host cells. The results showed decrease of the median relative abundance of viral contigs of classified eukaryotic viruses below 0.01%. The corresponding virome profiles showed dilution rate dependency, a reproducibility between biological replicates, and maintained high diversity regarding both the human and mouse inocula. This proof-of-concept cultivation approach may constitute the first step of developing novel therapeutic tools with high reproducibility and with low risk of infection from the donor material to target gut-related diseases.

Deciphering the pathogenic risks of microplastics as emerging particulate organic matter in aquatic ecosystem

Microplastics are accumulating rapidly in aquatic ecosystems, providing habitats for pathogens and vectors for antibiotic resistance genes (ARGs), potentially increasing pathogenic risks. However, few studies have considered microplastics as particulate organic matter (POM) to elucidate their pathogenic risks and underlying mechanisms. Here, we performed microcosm experiments with microplastics and natural POM (leaves, algae, soil), thoroughly investigating their distinct effects on the community compositions, functional profiles, opportunistic pathogens, and ARGs in Particle-Associated (PA) and Free-Living (FL) bacterial communities. We found that both microplastics and leaves have comparable impacts on microbial community structures and functions, enriching opportunistic pathogens and ARGs, which may pose potential environmental risks. These effects are likely driven by their influences on water properties, including dissolved organic carbon, nitrate, DO, and pH. However, microplastics uniquely promoted pathogens as keystone species and further amplified their capacity as hosts for ARGs, potentially posing a higher pathogenic risk than natural POM. Our research also emphasized the importance of considering both PA and FL bacteria when assessing microplastic impacts, as they exhibited different responses. Overall, our study elucidates the role and underlying mechanism of microplastics as an emerging POM in intensifying pathogenic risks of aquatic ecosystems in comparison with conventional natural POM.

Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes

For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. However, the 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other nearly-universal prokaryotic marker genes as the number of gene sequences increases in reference databases. This trend was strongly correlated with how represented a taxonomic group was in the database and indicates that, at the gene-level, the boundaries between many species might be fuzzy. Through our study, we argue that any approach that relies on a single marker to distinguish bacterial taxa is fraught even if some markers appear to be discriminative in current databases.

Identification of genus Deinococcus strains by PCR detection using the gyrB gene and its extension to Bacteria domain

In radiation-resistant bacteria belonging to the genus Deinococcus, transposition events of insertion sequences (IS elements) leading to phenotypic changes from a reddish color to white were detected following exposure to gamma irradiation and hydrogen peroxide treatment. This change resulted from the integration of IS elements into the phytoene desaturase gene, a key enzyme in the carotenoid biosynthesis pathway. To facilitate species identification and distinguish among Deinococcus strains, the gyrB gene encoding the B subunit of DNA gyrase was utilized. The s gnificance of the gyrB gene is well recognized not only in genome replication through the regulation of supercoiling but also in phylogenetic analysis providing support for 16S rRNA-based identification. Its mutation rate surpasses that of the 16S rRNA gene, offering greater resolution between closely related species, particularly those exhibiting >99% similarity. In this study, phylogenetic analysis was conducted comparing the 16S rRNA and gyrB gene sequences of Deinococcus species. Species-specific and genus-specific primers targeting Deinococcus species were designed and experimentally validated for selective amplification and rapid identification of the targeted species. This approach allows for the omission of 16S rRNA sequencing in the targeted Deinococcus species. Therefore, the gyrB gene is useful for identifying bacterial species and genus-level detection from individual microbes or microbial consortia using specialized primer sets for PCR amplification.

Gut microbiome and metabolic pathways linked to sleep quality

Sleep quality is a vital determinant of human health as sleep disorders are associated with cognitive deficits, and chronic sleep deprivation is associated with a broad range of health complications. Previous studies on the association between the gut microbiome and sleep quality have been constrained by small sample sizes or have focused on specific sleep disorders, thus yielding inconsistent results. Herein, we investigated the relationship between microbial composition and sleep quality in a cohort of 159 Koreans. Sleep quality was measured using the Pittsburgh Sleep Quality Index (PSQI), determined through a self-administered questionnaire. Gut microbiome analyses were performed using 16S rRNA amplicons. We found no direct correlation between microbial alpha diversity metrics and sleep; however, we identified differences in beta diversity among sleep quality groups (with a PSQI score > 5 indicating poor sleep quality and PSQI ≤5 indicating good sleep quality). We also found differential microbial signatures (Bacteroides, Prevotella 9, and Faecalibacterium) among the groups. Furthermore, functional metabolic pathway profiles revealed significant linear correlations of the L-arginine and L-tryptophan biosynthetic pathways as well as 4-aminobutanoate degradation with sleep status. In particular, Faecalibacterium prausnitzii, which harbors these metabolic pathways, showed differences between sleep quality groups and a linear association with sleep quality scores and was thus identified as the species most strongly associated with sleep status. This study provides a significant advance in our understanding of the relationship between gut microbiota and sleep regulation. The current findings provide a basis for further research into potential therapeutic strategies for sleep disorders targeting the gut microbiome.

Augmenting bacterial similarity measures using a graph-based genome representation

Relationships between bacterial taxa are traditionally defined using 16S rRNA nucleotide similarity or average nucleotide identity. Improvements in sequencing technology provide additional pairwise information on genome sequences, which may provide valuable information on genomic relationships. Mapping orthologous gene locations between genome pairs, known as synteny, is typically implemented in the discovery of new species and has not been systematically applied to bacterial genomes. Using a data set of 378 bacterial genomes, we developed and tested a new measure of synteny similarity between a pair of genomes, which was scaled onto 16S rRNA distance using covariance matrices. Based on the input gene functions used (i.e., core, antibiotic resistance, and virulence), we observed varying topological arrangements of bacterial relationship networks by applying (i) complete linkage hierarchical clustering and (ii) K-nearest neighbor graph structures to synteny-scaled 16S data. Our metric improved clustering quality comparatively to state-of-the-art average nucleotide identity metrics while preserving clustering assignments for the highest similarity relationships. Our findings indicate that syntenic relationships provide more granular and interpretable relationships for within-genera taxa compared to pairwise similarity measures, particularly in functional contexts.

IMPORTANCE

Given the prevalence and necessity of the 16S rRNA measure in bacterial identification and analysis, this additional analysis adds a functional and synteny-based layer to the identification of relatives and clustering of bacteria genomes. It is also of computational interest to model the bacterial genome as a graph structure, which presents new avenues of genomic analysis for bacteria and their closely related strains and species.

Microbial influence on the larval survival of Japanese eel Anguilla japonica: Antibiotic-mediated alterations and biomarker isolation

In rearing systems for the Japanese eel Anguilla japonica, although it is assumed that microorganisms influence larval survival and mortality, particularly during the early stages of growth, the effects of bacterial communities on larval survival have yet to be sufficiently determined. In this study, we compared the bacterial communities associated with larval survival at three stages of eel growth. To artificially alter bacterial communities and assess larval survival, eel larvae were treated with 11 types of antibiotic, and larval survival and bacterial characteristics were compared between the antibiotic-treated and antibiotic-free control groups. Throughout the three growth stages, eels treated with four antibiotics (polymyxin B, tetracycline, novobiocin, and erythromycin) had survival rates higher than those in the control groups. The bacterial communities of surviving larvae in the control and antibiotic groups and dead larvae in the control groups were subsequently analyzed using 16S rRNA gene amplicon sequencing. PERMANOVA analysis indicated that these three larval groups were characterized by significantly different bacterial communities. We identified 14 biomarker amplicon sequence variants (ASVs) of bacterial genera such as Oceanobacter, Alcanivorax, Marinobacter, Roseibium, and Sneathiella that were enriched in surviving larvae in the antibiotic treatment groups. In contrast, all four biomarker ASVs enriched in dead larvae of the control groups were from bacteria in the genus Vibrio. Moreover, 52 bacterial strains corresponding to nine biomarkers were isolated using a culture method. To the best of our knowledge, this is the first study to evaluate the bacterial communities associated with the survival and mortality of larvae in during the early stages of Japanese eel growth and to isolate biomarker bacterial strains. These findings will provide valuable insights for enhancing larval survival in the eel larval rearing systems from a microbiological perspective.

Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment

Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at the within-species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode.

The "Dry-Lab" Side of Food Authentication: Benchmark of Bioinformatic Pipelines for the Analysis of Metabarcoding Data

Next Generation Sequencing Technologies (NGS), particularly metabarcoding, are valuable tools for authenticating foodstuffs and detecting eventual fraudulent practices such as species substitution. This technique, mostly used for the analysis of prokaryotes in several environments (including food), is in fact increasingly applied to identify eukaryotes (e.g., fish, mammals, avian, etc.) in multispecies food products. Besides the "wet-lab" procedures (e.g., DNA extraction, PCR, amplicon purification, etc.), the metabarcoding workflow includes a final "dry-lab" phase in which sequencing data are analyzed using a bioinformatic pipeline (BP). BPs play a crucial role in the accuracy, reliability, and interpretability of the metabarcoding results. Choosing the most suitable BP for the analysis of metabarcoding data could be challenging because it might require greater informatics skills than those needed in standard molecular analysis. To date, studies comparing BPs for metabarcoding data analysis in foodstuff authentication are scarce. In this study, we compared the data obtained from two previous studies in which fish burgers and insect-based products were authenticated using a customizable, ASV-based, and command-line interface BP (BP1) by analyzing the same data with a customizable but OTU-based and graphical user interface BP (BP2). The final sample compositions were compared statistically. No significant difference in sample compositions was highlighted by applying BP1 and BP2. However, BP1 was considered as more user-friendly than BP2 with respect to data analysis streamlining, cost of analysis, and computational time consumption. This study can provide useful information for researchers approaching the bioinformatic analysis of metabarcoding data for the first time. In the field of food authentication, an effective and efficient use of BPs could be especially useful in the context of official controls performed by the Competent Authorities and companies' self-control in order to detect species substitution and counterfeit frauds.

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments

BACKGROUND

Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases.

METHODS

To overcome these challenges, we developed methods to broaden FVT's clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline.

RESULTS

FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy.

CONCLUSIONS

This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract.

Dispersant addition, but not nutrients, stimulated blooms of multiple hydrocarbonoclastic genera in nutrient-replete coastal marine surface waters

The range of impacts of chemical dispersants on indigenous marine microbial communities and their activity remains poorly constrained. We tested the response of nearshore surface waters chronically exposed to oil leakage from a downed platform and supplied with nutrients by the Mississippi River to Corexit dispersant and nutrient additions. As assessed using 14C-labeled tracers, hexadecane mineralization potential was orders of magnitude higher in all unamended samples than in previously assessed bathypelagic communities. Nutrient additions stimulated microbial mortality but did not affect community composition and had no generalizable effect on hydrocarbon mineralization potential. By contrast, Corexit amendments caused a rapid shift in community composition and a drawdown of inorganic nitrogen and orthophosphate though no generalizable effect on hydrocarbon mineralization potential. The hydrocarbonoclastic community's response to dispersants is largely driven by the relative availability of organic substrates and nutrients, underscoring the role of environmental conditions and multiple interacting stressors on hydrocarbon degradation potential.

Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible

Fungi is a highly diverse group of eukaryotic organisms that live under an extremely wide range of environmental conditions. Nowadays, there is a fundamental focus on observing how biodiversity varies on different spatial scales, in addition to understanding the environmental factors which drive fungal biodiversity. Metabarcoding is a high-throughput DNA sequencing technology that has positively contributed to observing fungal communities in environments. While the DNA sequencing data generated from metabarcoding studies are available in public archives, this valuable data resource is not directly usable for fungal biodiversity investigation. Additionally, due to its fragmented storage and distributed nature, it is not immediately accessible through a single user interface. We developed the MycoDiversity DataBase User Interface (https://mycodiversity.liacs.nl) to provide direct access and retrieval of fungal data that was previously inaccessible in the public domain. The user interface provides multiple graphical views of the data components used to reveal fungal biodiversity. These components include reliable geo-location terms, the reference taxonomic scientific names associated with fungal species and the standard features describing the environment where they occur. Direct observation of the public DNA sequencing data in association with fungi is accessible through SQL search queries created by interactively manipulating topological maps and dynamic hierarchical tree views. The search results are presented in configurable data table views that can be downloaded for further use. With the MycoDiversity DataBase User Interface, we make fungal biodiversity data accessible, assisting researchers and other stakeholders in using metabarcoding studies for assessing fungal biodiversity.

A novel microbial community restructuring strategy for enhanced hydrogen production using multiple pretreatments and CSTR operation

To achieve rapid enrichment of the targeted hydrogen-producing bacterial population and reconstruction of the microbial community in the biological hydrogen-producing reactor, the activated sludge underwent multiple pretreatments using micro-aeration, alkaline treatment, and heat treatment. The activated sludge obtained from the multiple pretreatments was inoculated into the continuous stirred tank reactor (CSTR) for continuous operations. The community structure alteration and hydrogen-producing capability of the activated sludge were analyzed throughout the operation of the reactor. We found that the primary phyla in the activated sludge population shifted to Proteobacteria, Firmicutes, and Bacteroidetes, which collectively accounted for 96.69% after undergoing several pretreatments. This suggests that the multiple pretreatments facilitated in achieving the selective enrichment of the fermentation hydrogen-producing microorganisms in the activated sludge. The CSTR start-up and continuous operation of the biological hydrogen production reactor resulted in the reactor entering a highly efficient hydrogen production stage at influent COD concentrations of 4000 mg/L and 5000 mg/L, with the highest hydrogen production rate reaching 8.19 L/d and 9.33 L/d, respectively. The main genus present during the efficient hydrogen production stage in the reactor was Ethanoligenens, accounting for up to 33% of the total population. Ethanoligenens exhibited autoaggregation capabilities and a superior capacity for hydrogen production, leading to its prevalence in the reactor and contribution to efficient hydrogen production. During high-efficiency hydrogen production, flora associated with hydrogen production exhibited up to 46.95% total relative abundance. In addition, redundancy analysis (RDA) indicated that effluent pH and COD influenced the distribution of the primary hydrogen-producing bacteria, including Ethanoligenens, Raoultella, and Pectinatus, as well as other low abundant hydrogen-producing bacteria in the activated sludge. The data indicates that the multiple pretreatments and reactor's operation has successfully enriched the hydrogen-producing genera and changed the community structure of microbial hydrogen production.

Multi-omics unveils tryptophan metabolic pathway as a key pathway influencing residual feed intake in Duroc swine

The genetic trait of residual feed intake (RFI) holds considerable importance in the swine industry. Recent research indicates that the gut microbiota of pigs plays a pivotal role in the manifestation of the RFI trait. Nevertheless, the metabolic pathways involved in the functioning of these microorganisms remain elusive. Thus, based on the ranking of the RFI trait in Duroc pigs, the present study selected the top 10 and bottom 10 pigs as the experimental subjects. The distribution and metabolite differences of cecal microbiota were analyzed using 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. The low RFI cecal group was named LRC, and the high RFI cecal group was named HRC. The results indicate that the LRC group had lower RFI, feed conversion ratio (FCR), average daily feed intake (ADFI) (p < 0.001), and thinner backfat (p < 0.05) compared with the HRC group. We simultaneously recorded the foraging behavior as well, the LRC group had a significant increase in total time spent at the feeder per day (TPD) (p < 0.05) and a significant increase in average feed intake per mins (AFI) and the number of visits to the feeder per day (NVD) compared to the HRC group (p < 0.001). Clostridium_XVIII, Bulleidia, and Intestinimonas were significantly enriched in the LRC group (p < 0.01), while Sutterella, Fusobacterium, and Bacteroides were significantly increased in the HRC group (p < 0.01). In the metabolome, we detected 390 (248 metabolites up and 142 down in the LRC compared with HRC), and 200 (97 metabolites up and 103 down in the LRC compared with HRC) differential metabolites in positive and negative ionization modes. The comprehensive analysis found that in the LRC group, Escherichia and Eubacterium in the gut may increase serotonin content, respectively. Bacteroides may deplete serotonin. We suggest that the RFI may be partly achieved through tryptophan metabolism in gut microbes. In individuals with low RFI, gut microbes may enhance feed efficiency by enhancing host synthesis and metabolism of tryptophan-related metabolites.

A survey of BWT variants for string collections

MOTIVATION

In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have been developed for computing the BWT of string collections. While the focus has been on improving efficiency, both in space and time, the exact definition of the BWT employed has not been at the center of attention. As we show in this paper, the different tools in use often compute non-equivalent BWT variants: the resulting transforms can differ from each other significantly, including the number r of runs, a central parameter of the BWT. Moreover, with many tools, the transform depends on the input order of the collection. In other words, on the same dataset, the same tool may output different transforms if the dataset is given in a different order.

RESULTS

We studied 18 dedicated tools for computing the BWT of string collections and were able to identify 6 different BWT variants computed by these tools. We review the differences between these BWT variants, both from a theoretical and from a practical point of view, comparing them on 8 real-life biological datasets with different characteristics. We find that the differences can be extensive, depending on the datasets, and are largest on collections of many similar short sequences. The parameter r, the number of runs of the BWT, also shows notable variation between the different BWT variants; on our datasets, it varied by a multiplicative factor of up to 4.2.

AVAILABILITY

Source code and scripts to replicate the results and download the data used in the article are available at https://github.com/davidecenzato/BWT-variants-for-string-collections.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria

BACKGROUND

The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line.

RESULTS

We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community.

CONCLUSION

Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.

Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies

BACKGROUND

In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.

RESULTS

Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.

CONCLUSIONS

Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.