Human Body Sites Research Articles

Fusobacterium sphaericum sp. nov. , isolated from a human colon tumor, adheres to colonic epithelial cells and induces IL-8 secretion.

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. ( Fs ), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe Veillonella dispar in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate.

Veillonella spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal Veillonella reside in the human body site where lactate level is, however, limited for Veillonella growth. In this study, nitrate was shown to promote the anaerobic growth of Veillonella in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote Veillonella dispar growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled V. dispar to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways via reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal V. dispar utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects via microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. Veillonella are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by V. dispar to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of V. dispar further suggested the potential roles of nitrate and Veillonella in the promotion of human health.

Multicenter Candida auris outbreak caused by azole-susceptible clade IV in Pernambuco, Brazil.

Candida auris is an emerging multidrug-resistant yeast, frequently causing outbreaks in health care facilities. The pathogen persistently colonises human skin and inanimate surfaces such as catheters, aiding to its spread. Moreover, colonisation is a risk factor to develop invasive infection. We investigated 61 C. auris strains isolated from non-sterile human body sites (n = 53) and the hospital environment (n = 8), originating from four different centres in a single Brazilian state. Antifungal susceptibility testing (AFST) against common antifungals was performed, and resistance-associated genes were evaluated. Genetic relatedness was investigated with short tandem repeat (STR) genotyping and validated with whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. Antifungal susceptibility testing demonstrated that all isolates were susceptible to azoles, echinocandins and amphotericin B. No mutations were detected in ERG11 and FKS1 genes. With STR typing, isolates were allocated to clade IV and appeared closely related. This was confirmed by WGS SNP analysis of 6 isolates, which demonstrated a maximal difference of only 41 SNPs between these strains. Furthermore, the Brazilian isolates formed a distinct autochthonous branch within clade IV, excluding recent introductions from outside the country. A molecular clock analysis of clade IV isolates from various countries suggests that early in the previous century there was a unique event causing environmental spread of a C. auris ancestor throughout the Latin-American continent, followed by human introduction during the last decades. We report the emergence of C. auris patient colonisation in multiple centres by fluconazole-susceptible clade IV close-related strains in Pernambuco State, Brazil.

Comparative analysis of the antimicrobial resistance and virulence traits in ESBL-producing-Klebsiella pneumoniae ST307 strains colonizing the gastrointestinal tract and causing a fatal bloodstream infection in a leukemia patient

Klebsiella pneumoniae is an opportunistic pathogen that can colonize the gastrointestinal tract (GIT) of humans. The mechanisms underlying the successful translocation of this pathogen to cause extra-intestinal infections remain unknown, although virulence and antimicrobial resistance traits likely play significant roles in the establishment of infections. We investigated K. pneumoniae strains isolated from GIT colonization (strains Kp_FZcol-1, Kp_FZcol-2 and Kp_FZcro-1) and from a fatal bloodstream infection (strain Kp_HM-1) in a leukemia patient. All strains belonged to ST307, carried a transferable IncF plasmid containing the blaCTX-M-15 gene (pKPN3–307 TypeA-like plasmid) and showed a multidrug-resistance phenotype. Phylogenetic analysis demonstrated that Kp_HM-1 was more closely related to Kp_FZcro-1 than to the other colonizing strains. The Kp_FZcol-2 genome showed 81 % coverage with the Kp_HM-1 246,730 bp plasmid (pKp_HM-1), lacking most of its putative virulence genes. Searching public genomes with similar coverage, we observed the occurrence of this deletion in K. pneumoniae ST307 strains recovered from human colonization and infection in different countries. Our findings suggest that strains lacking the putative virulence genes found in the pKPN3–307 TypeA plasmid are still able to colonize and infect humans, highlighting the need to further investigate the role of these genes for the adaptation of K. pneumoniae ST307 in distinct human body sites.

Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system.

This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.

Prophages: an integral but understudied component of the human microbiome.

Phages integrated into a bacterial genome - called prophages - continuously monitor the vigour of the host bacteria to determine when to escape the genome and to protect their host from other phage infections, and they may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies have focused on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. To address this gap in our knowledge, we compared the prophages identified in 14 987 bacterial genomes isolated from human body sites to characterize prophage DNA in the human microbiome. Here, we show that prophage DNA is ubiquitous, comprising on average 1-5 % of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.

Human associated Archaea: a neglected microbiome worth investigating.

The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.

Bacteriocin-Producing Probiotic Lactic Acid Bacteria against Hospital Strains of Staphylococcus aureus and Escherichia coli

It is now accepted that the human microbiome plays a key role in human health, and disturbances in the microbiome can cause or aggravate a range of diseases, from metabolic to immune disorders and mood disorders [1]. In addition, microbiota imbalance or dysbiosis may arise due to careless use of antibiotics in humans and animals, leading to the emergence of antibiotic-resistant bacteria that may compromise the effectiveness of antibiotics, so there is an urgent need to identify and develop new strategies to combat antibiotics resistance [2,3]. So far, probiotics are considered as perspective alternatives to antibiotics [4]. Probiotics are defined by the FAO/WHO as “Live microorganisms which when administered in adequate amounts confer a health benefit on the host” and they are successfully used for preservation of the microbial community [5].Moreover, bacteriocin-producing commensal microbes have the capacity to eliminate specific colonizing pathogens from various human body sites, and, as many bacteriocins have only narrow activity ranges they can be used for precision therapy and infections prevention [6]. Lactic acid bacteria, particularly lactobacilli, are the best known probiotics that modulate the immune system, and produce significant amounts of bioactive compounds, including bacteriocins, to eliminate pathogens and limit the clinical effects of antibiotic use [7, 8].

ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome.

The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.

The first completed genome of species Prevotella bivia, assembled from a clinically derived strain PLW0727

Prevotella bivia is a species that commonly colonizes various human body sites, and it is associated with lots of human infections. However, until now, no complete genome sequence of this species has been published. Here, we assembled the first complete genome of P. bivia from a clinically derived strain PLW0727, to characterize its general genomic features, and to profile the capacity in encoding antibiotic resistance and virulence factors. Whole-genome sequencing was performed using Illumina and Nanopore platforms. Hybrid assembly was conducted using flye v2.9.1 and Unicycler v0.4.9b. Assembly completeness was assessed using CheckM v1.0.12. Comprehensive genome annotation was performed using eggNOG-mapper v2.1.5 and PATRIC v3.6.10. The complete genome of PLW0727 consists of two circular chromosomes, chr1 and chr2, exhibiting a completeness of 99.66%, a G+C content of 39.5%, and a total size of 2.43 Mb. Chr1 and chr2 have lengths of 1 272 652 bp and 1 155 021 bp, harbouring 1 132 CDSs and 1 055 CDSs, respectively. Completion of the genome significantly reduced the proportion of hypothetical CDS annotations compared with the draft genomes. A gene-encoding antibiotic resistance to beta-lactams (i.e., cfxA3) has been annotated in chr2. By providing the genome sequence, strain PLW0727 was identified as a human pathogen with a probability of 0.614 using the PathogenFinder. Furthermore, genes involved in virulence-related functions, including host cell adherence and capsule immune modulation were also annotated. This study assembles the first complete genome for P. bivia, providing valuable genomic insights into its phylogeny, pathogenicity, and antibiotic resistance. These findings have important implications for the clinical management and prevention of P. bivia infections.

Targeting the Gut-Eye Axis: An Emerging Strategy to Face Ocular Diseases.

The human microbiota refers to a large variety of microorganisms (bacteria, viruses, and fungi) that live in different human body sites, including the gut, oral cavity, skin, and eyes. In particular, the presence of an ocular surface microbiota with a crucial role in maintaining ocular surface homeostasis by preventing colonization from pathogen species has been recently demonstrated. Moreover, recent studies underline a potential association between gut microbiota (GM) and ocular health. In this respect, some evidence supports the existence of a gut-eye axis involved in the pathogenesis of several ocular diseases, including age-related macular degeneration, uveitis, diabetic retinopathy, dry eye, and glaucoma. Therefore, understanding the link between the GM and these ocular disorders might be useful for the development of new therapeutic approaches, such as probiotics, prebiotics, symbiotics, or faecal microbiota transplantation through which the GM could be modulated, thus allowing better management of these diseases.

The Effect of Cupressus arizonica Fruit Ethyl Alcoholic Extract Toward some Bacterial Species that Isolated from Different Infections of Human Body’s Sites

Cupressus arizonica composed from several compounds such as quinones, flavonoids, saponins, terpenes,, tannins and phenolic compounds. polyphenolic compounds considerable as antioxidant potentials which related to the human health. The ethyl 95% extract of Cupressus arizonica in different concentrations were measured inhibited against five bacterial isolates (E. coli, Klebsiella pneumonia, Aeromonas sp., Salmonella sp. and Staphylococcus aureus) from different sites of human body. and measured this inhibitory effect with different antibiotic discs such as (Ciprofloxacin 10 µg, Norfloxacin (10 µg), Vancomycin (30µg), Lincomycin (15µg), Imipenem (10 µg) and (25 µg), Lincomycin (15µg) and Trimethoprim /Sulfamethaxazole (25 µg). Cupressus arizonica fruit ethyl extract in 100% concentration toward different species of bacteria like E. coli, Klebsiella pneumonia, Aeromonas sp, Salmonella sp and Staphylococcus aureus. At different inhibition zones 11, 25,10,15, 21 µg/ ml respectively for each one of them compared with some antibiotics were used in this study.Minimum Inhibitory Concentration (MIC) of Cupressus arizonica ethanol extract for bacteria E.coli, Klebsiella pneumonia, Aeromonas sp., Salmonella sp. and Staphylococcus aureus. The MIC of Cupressus arizonica affected on E.coli Klebsiella pneumonia, Aeromonas sp. and Staphylococcus aureus were 12.5 µg/ ml. The MIC of Cupressus arizonica ethanol extract for Salmonella sp. was at 50 µg/ ml. the inhibition means of Cupressus arizonica fruit alcoholic extract toward bacterial isolates recorded lowest mean 8.6 at concentration 75% against E. coli bacteria, but the highest mean was at 21 at concentration 100% towards Staphylococcus aureus, while other concentration means distributed among bacterial isolates in different effects.

Emerging Nosocomial Trichosporon asahii in a Tertiary Hospital in Southern Saudi Arabia

Background: Trichosporon species are pathogenic yeasts that colonize diverse human body sites and cause superficial in addition to invasive trichosporonosis, especially in immunosuppressed patients. The disease is an emerging health-care problem, as it has shown a noticeable increase in recent years. The leading risk factors are antibiotic use, invasive medical equipment, and chemotherapy. Informed evidence on the disease and its causal agent is needed. Objective: Presentation of clinical cases caused by Trichosporon sp. and identification of isolates recovered from various specimens in Aseer Central Hospital setting. Materials and Methods: The study analyzed fungal cultures (n = 20) from different clinical specimens submitted on a routine basis from hospital wards for general microbiological investigation at Aseer Central Hospital, Abha, Saudi Arabia (2021–2023). Mycologically proven trichosporonosis cases were initially identified by desktop methods, automated Vitek 2, and confirmed by sequence analysis of the ribosomal targets, namely the large-subunit RNA gene (D1–D2 region) and internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions), patients were treated with fluconazole, and treatment outcomes were recorded. Results: Clinical features and culture results confirmed trichosporonosis caused by Trichosporon asahii with different clinical presentations. The majority of the cases were urinary tract (44%), followed by skin (28%) and respiratory tract (12%). All trichosporonosis cases responded to fluconazole. The neighbor-joining phylogenetic tree based on the rRNA regions and ITS and comparative analysis using GenBank reference data showed the association of our strains to the reference T. asahii clade, closely related to T. faecale and T. insectorum but different from other species. Conclusions: The study offered accurate species identification of the Trichosporon isolates by routine phenotypic tests as well as sequence-based techniques. Urinary tract infections were the most common manifestation of the infection, followed by skin and then respiratory tract infections. The cases of trichosporonosis responded well to fluconazole treatment. T. asahii is possibly underreported and should be considered in routine diagnostic investigations, notably in nosocomial infections.

Insights on Current Strategies to Decolonize the Gut from Multidrug-Resistant Bacteria: Pros and Cons.

In the last decades, we have witnessed a steady increase in infections caused by multidrug-resistant (MDR) bacteria. These infections are associated with higher morbidity and mortality. Several interventions should be taken to reduce the emergence and spread of MDR bacteria. The eradication of resistant pathogens colonizing specific human body sites that would likely cause further infection in other sites is one of the most conventional strategies. The objective of this narrative mini-review is to compile and discuss different strategies for the eradication of MDR bacteria from gut microbiota. Here, we analyse the prevalence of MDR bacteria in the community and the hospital and the clinical impact of gut microbiota colonisation with MDR bacteria. Then, several strategies to eliminate MDR bacteria from gut microbiota are described and include: (i) selective decontamination of the digestive tract (SDD) using a cocktail of antibiotics; (ii) the use of pre and probiotics; (iii) fecal microbiota transplantation; (iv) the use of specific phages; (v) engineered CRISPR-Cas Systems. This review intends to provide a state-of-the-art of the most relevant strategies to eradicate MDR bacteria from gut microbiota currently being investigated.

Distribution of Candida infections in patients and evaluation of the synergic interactions of some drugs against emerging fluconazole- and caspofungin-resistant C. auris

Pathogenic multidrug-resistantCandidaspecies are considered some of the most important health risks. This work aimed to evaluate and monitor the prevalence of the human pathogenic Candida strains isolated from patients in King Fahd Medical City (KFMD), Riyadh, Saudi Arabia, and to evaluate the synergy of some antimicrobial agents against Candida species’ resistance to antifungal drugs. The retrospective analysis, identification using biochemical tests, minimal inhibitory concentrations using E-tests, determination of the fraction inhibitory concentration index value for synergic testing, and simulation of 100 experiments using Monte Carlo simulation methods were performed according to standard protocols. The findings showed that all age groups of males and females can be infected by Candida species; furthermore, human pathogenic Candida species can be isolated from several clinical samples and different human body sites. The minimal inhibitory concentration results showed that many multidrug-resistant Candida strains, such as C. albicans, emerged in 2020 compared to 2018. Candida albicans remains the most important pathogen among all Candia species, found in 51.7 % and 42.4 % of the isolates in 2018 and 2020, respectively. In 2018, many isolates of C albicans showed resistance to itraconazole, fluconazole, anidulafungin, amphotericin B, ketoconazole, voriconazole, caspofungin, and flucytosine. In 2018, all C. auris isolates (N = 94) were resistant to fluconazole, and more than 85 % (N = 76) of C. albicans isolates were resistant to itraconazole, while only 5.9 % (N = 2) were resistant in 2018. The study concluded that the resistance to antifungal drugs among pathogenic yeasts is increasing and constantly changing and that surveillance of these pathogens must continue. Also, the synergy between drugs remains an appropriate option for confronting this risk, especially between natural extracts and drugs. Despite the lack of evidence for any antifungal and antibacterial drug's ability to synergistically suppress the fluconazole- and caspofungin-resistant C. auris strains diagnosed in this study, the surveillance and synergic tactics continue to be viable options for dealing with these human pathogenic yeasts.

S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota.

Compelling evidence points to the critical role of bioactive extra-virgin olive oil (EVOO) phenolics and gut microbiota (GM) interplay, but reliable models for studying the consequences thereof remain to be developed. Herein, we report an optimized ex vivo fecal anaerobic fermentation model to study the modulation of GM by the most bioactive EVOO phenolic S-(-)-oleocanthal (OC), and impacts therefrom, focusing on OC biotransformation in the gut. This model will also be applicable for characterization of GM interactions with other EVOO phenolics, and moreover, for a broadly diverse range of bioactive natural products. The fecal fermentation media and time, and mouse type and gender, were the major factors varied and optimized to provide better understanding of GM-OC interplay. A novel resin entrapment technique (solid-phase extraction) served to selectively entrap OC metabolites, degradation products, and any remaining fraction of OC while excluding interfering complex fecal medium constituents. The effects of OC on GM compositions were investigated via shallow shotgun DNA sequencing. Robust metabolome analyses identified GM bacterial species selectively altered (population numbers/fraction) by OC. Finally, the topmost OC-affected gut bacterial species of the studied mice were compared with those known to be extant in humans and distributions of these bacteria at different human body sites. OC intake caused significant quantitative and qualitative changes to mice GM, which was also comparable with human GM. Results clearly highlight the potential positive health outcomes of OC as a prospective nutraceutical.

Highly Sensitive Strain Sensor Based on Microfiber Coupler for Wearable Photonics Healthcare

Flexible strain sensors are essential components of wearable smart devices that perceive and respond to strain stimulations. However, the sensitivity and response time of most sensors require further improvement to detect subtle strains related to human bodies. Herein, an ultrasensitive flexible optical sensor with fast response time has been built based on a microfiber coupler encapsulated in polydimethylsiloxane. Benefiting from dramatic change of coupling ratio of the microfiber coupler under weak strain, this flexible strain sensor exhibits ultrahigh strain sensitivity (gauge factor, GF = 900), low detection limit (0.001%), ultrafast response time (<0.167 ms), wide sensing range (0.45%), and superior durability and stability (>10 000 cycles). Real‐time capturing and recognizing of respiration, broadband sound signals, and pulse waves at different sites of human body have been demonstrated based on this highly sensitive microfiber coupler sensor. Moreover, simultaneous detection of the wrist pulse and human voice has been achieved based on the frequency division multiplexing technology. This flexible photonics strain sensor could serve as the prototype of ultrasensitive flexible optical sensors with fast response time for the development of high performance and wearable healthcare devices.

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

BackgroundTaxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both “known” and “unknown” species based on a set of select marker genes.ResultsWe present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6–11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43–63%) or even the majority (pig, fish, cattle: 60–80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies.ConclusionsWe developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs.EtaL3gdjB5XhyYuYaq3JvNVideo

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.

Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.

The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites

BackgroundHuman endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, mounting evidence shows that several expressed HERVs do exert biological functions. Here, we systematically characterize physiologically expressed HERVs and examine whether they may give insight into the molecular fundamentals of human development and disease.ResultsWe systematically identify 13,889 expressed HERVs across normal body sites and demonstrate that they are expressed in body site-specific patterns and also by sex, ethnicity, and age. Analyzing cis-ERV-related quantitative trait loci, we find that 5435 hervRNAs are regulated by genetic variants. Combining this with a genome-wide association study, we elucidate that the dysregulation of expressed HERVs might be associated with various complex diseases, particularly neurodegenerative and psychiatric diseases. We further find that physiologically activated hervRNAs are associated with histone modifications rather than DNA demethylation.ConclusionsOur results present a locus-specific landscape of physiologically expressed hervRNAs, which represent a hidden layer of genetic architecture in development and disease.