Single-cell approaches in human microbiome research.

Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional variation of the human microbiome and its impact on host processes. The next increase in resolution will come by understanding the role of low-abundant and less-prevalent bacteria and the study of individual cell behaviors that underlie the complexity of microbial ecosystems. To this aim, single-cell techniques are being rapidly developed to isolate, culture, and characterize the genomes and transcriptomes of individual microbes in complex communities. Here, we discuss how these single-cell technologies are providing unique insights into the biology and behavior of human microbiomes.

Elevated rates of horizontal gene transfer in the industrialized human microbiome.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Taxonomic and phenotypic analysis of bifidobacteria isolated from IBD patients as potential probiotic strains.

BACKGROUND: Inflammatory Bowel Diseases (IBD) are a major public health issue with unclear aetiology. Changes in the composition and functionality of the intestinal microbiota are associated with these pathologies, including the depletion of strict anaerobes such as Feacalibacterium prausnitzii. Less evidence is observed for depletion in other anaerobes, among which bifidobacteria. This study characterized the taxonomic and functional diversity of bifidobacteria isolated from the human intestinal microbiota in active and non-active IBD patients by a culturomics approach and evaluated if these bifidobacteria might be used as probiotics for gut health. RESULTS: A total of 341 bifidobacteria were isolated from the intestinal microbiota of IBD patients (52 Crohn's disease and 26 ulcerative colitis patients), with a high proportion of Bifidobacterium dentium strains (28% of isolated bifidobacteria). In ulcerative colitis, the major species identified was B. dentium (39% of isolated bifidobacteria), in active and non-active ulcerative colitis. In Crohn's disease, B. adolescentis was the major species isolated from non-active patients (40%), while similar amounts of B. dentium and B. adolescentis were found in active Crohn's disease patients. The relative abundance of B. dentium was increased with age, both in Crohn's disease and ulcerative colitis and active and non-active IBD patients. Antibacterial capacities of bifidobacteria isolated from non-active ulcerative colitis against Escherichia coli LF82 and Salmonella enterica ATCC 14028 were observed more often compared to strains isolated from active ulcerative colitis. Finally, B. longum were retained as strains with the highest probiotic potential as they were the major strains presenting exopolysaccharide synthesis, antibacterial activity, and anti-inflammatory capacities. Antimicrobial activity and EPS synthesis were further correlated to the presence of antimicrobial and EPS gene clusters by in silico analysis. CONCLUSIONS: Different bifidobacterial taxonomic profiles were identified in the microbiota of IBD patients. The most abundant species were B. dentium, mainly associated to the microbiota of ulcerative colitis patients and B. adolescentis, in the intestinal microbiota of Crohn's disease patients. Additionally, the relative abundance of B. dentium significantly increased with age. Furthermore, this study evidenced that bifidobacteria with probiotic potential (antipathogenic activity, exopolysaccharide production and anti-inflammatory activity), especially B. longum strains, can be isolated from the intestinal microbiota of both active and non-active Crohn's disease and ulcerative colitis patients.

Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches.

Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders.

Impact on species' online attention when named after celebrities.

Celebrities can generate substantial attention and influence public interest in species. Using a large-scale examination of publicly available data, we assessed whether species across 6 taxonomic groups received more page views on Wikipedia when the species was named after a celebrity than when it was not. We conducted our analysis for 4 increasingly strict thresholds of how many average daily Wikipedia page views a celebrity had (1, 10, 100, or 1000 views). Overall, we found a high probability (0.96-0.98) that species named after celebrities had more page views than their closest relatives that were not named after celebrities, irrespective of the celebrity threshold. The multiplicative effect on species' page views was larger but more uncertain as celebrity page-view thresholds increased. The range for thresholds of 1 to 1000 was 1.08 (95% credible interval [CI] 1.00-1.18) to 1.76 (95% CI 0.96-2.80), respectively. The hierarchical estimates for the taxa tended to be positive. The strongest effects were for invertebrates, followed by amphibians, reptiles, fish, and mammals, whereas the weakest effect was for birds at lower page-view thresholds. Our results suggest that naming species after celebrities could be particularly significant for those belonging to taxonomic groups that are generally less popular than others (e.g., invertebrates). Celebrities may further influence the effectiveness of this marketing strategy, depending on their likability and connection to the species named after them. Eponyms may serve as a reminder of the disproportionate power dynamics between populations and some namesakes' untenable actions. However, they also provide an opportunity to recognize remarkable individuals and promote equity, inclusivity, and diversity in taxonomic practice. We encourage taxonomists to examine whether naming threatened species after celebrities could affect conservation support, especially for species that are otherwise typically overlooked by the public.

Impacto sobre la atención virtual de una especie si lleva el nombre de una celebridad Resumen Las celebridades pueden generar atención considerable e influir sobre el interés público por las especies. Usamos un análisis a gran escala de datos con disponibilidad pública para evaluar si las especies de seis grupos taxonómicos recibían más visitas en Wikipedia cuando el nombre de la especie provenía del de una celebridad que cuando no. Realizamos nuestro análisis en cuatro umbrales cada vez más estrictos de cuántas visitas diarias en promedio tenía la página de Wikipedia de una celebridad (1, 10, 100 or 1000 visitas). En general, descubrimos una probabilidad alta (0.96­0.98) de que las especies con nombres de celebridades tuvieran más visitas que sus parientes más cercanos que no tenían un nombre así, sin importar el umbral de la celebridad. El efecto multiplicativo sobre las visitas a la página de la especie fue mayor pero más incierto si incrementaba el umbral de visitas de la celebridad. El rango para los umbrales de 1 a 1000 fue de 1.08 (95% intervalo creíble [IC] 1.00­1.18) a 1.76 (95% IC 0.96­2.80) respectivamente. Los estimados jerárquicos para los taxones tuvieron una tendencia positiva. Los efectos más fuertes se presentaron en los invertebrados, seguidos de los anfibios, reptiles, peces y mamíferos, mientras que el efecto más débil fue para las aves en los umbrales de menor número de visitas. Nuestros resultados sugieren que nombrar a una especie con el nombre de una celebridad podría ser particularmente importante para aquellas que pertenecen a grupos taxonómicos que generalmente suelen ser menos populares que otros (invertebrados). Las celebridades podrían influir todavía más en la efectividad de esta estrategia de marketing, dependiendo de su popularidad y la conexión con la especie que lleva su nombre. Los epónimos pueden funcionar como recordatorios de las dinámicas disparejas de poder entre las poblaciones y las acciones indefendibles de algunos homónimos. Sin embargo, los epónimos también proporcionan la oportunidad para reconocer individuos destacados y promover la equidad, inclusividad y diversidad en la práctica taxonómica. Alentamos a que los taxónomos analicen si nombrar a una especie amenazada con el nombre de una celebridad podría afectar el apoyo a su conservación, especialmente para las especies que de otra manera suelen ser ignoradas por el público.

Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology.

The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.

A novel method for enrichment of Morganella morganii in fecal samples using designed culture medium.

Morganella morganii is a gram negative, facultative anaerobic rod-shaped bacterium, commonly found in environment and in the intestine of human, mammals, and reptiles as a part of their gut microbiome. M. morganii can cause Gram-negative folliculitis, black nail infection, acute retiform purpura, fetal demise, and subdural empyema. The increasing frequency of M. morganii infections generate the need for efficient methods to enrich the presence of M. morganii in clinical samples to make its detection easier. Culturomics aims to grow and maximize the number of culturable bacteria. Different methods are followed to maximize the growth of minority population of bacteria by disrupting the growth of bacteria which are present in higher concentration. This article presents a method for selective enriching the M. morganii in human fecal samples. This method includes prior incubation of fecal microbiota in an anaerobic environment, adding supplement like fecal water to give dormant bacteria a break to become active to grow to threshold concentration, and an enrichment stage which provides the additional opportunity of growing to M. morganii on the selective medium. This method also provides an ingenuous way for augmenting the growth of fecal M. morganii species.

A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification.

The demand for functional food is rising in tandem with the prevalence of chronic diseases. Probiotics play a crucial role in functional food development, yet their ability to confer health benefits to the host remains a topic of debate according to Food and Agriculture Organization/World Health Organization requirements. The application of culturomics, innovative isolation techniques, within the realm of probiotics is increasingly deemed essential for fully harnessing the latent potential of microbial reservoirs. Nevertheless, its application remains confined predominantly to human fecal sources. Following the integration of probiogenomics, significant advancements have been made in the safety assessment of probiotics. However, the adoption of novel probiotic microorganisms has yet to match the requisite pace. Progress in research concerning host-probiotic interactions by employing omics technologies, particularly in animal models, is notable. Nonetheless, the comprehensive elucidation of mechanisms of action and human trial studies are lagging behind. Additionally, the viability of probiotics, spanning from their production as functional foods to their transit to the human colon, has markedly improved through encapsulation techniques. Nevertheless, opportunities for exploration persist regarding alternative coating materials and diverse encapsulation methodologies. Furthermore, there is a discernible transition in the domain of probiotic-based functional foods, shifting away from a primarily dairy-centric focus toward inclusion in a broader array of food categories. This comprehensive review addresses critical issues ranging from isolation sources and novel techniques to the final functional food developments. while doing so, it explores probiogenomics applications for probiotic characterization, investigations into host-probiotic interactions, and strategies for probiotic stabilization under harsh environmental conditions.

Social media and social impact assessment: Evolving methods in a shifting context.

Among many by-products of Web 2.0 come the wide range of potential image and text datasets within social media and content sharing platforms that speak of how people live, what they do, and what they care about. These datasets are imperfect and biased in many ways, but those flaws make them complementary to data derived from conventional social science methods and thus potentially useful for triangulation in complex decision-making contexts. Yet the online environment is highly mutable, and so the datasets are less reliable than censuses or other standard data types leveraged in social impact assessment. Over the past decade, we have innovated numerous methods for deploying Instagram datasets in investigating management or development alternatives. This article synthesizes work from three Canadian decision contexts - hydroelectric dam construction or removal; dyke realignment or wetland restoration; and integrating renewable energy into vineyard landscapes - to illustrate some of the methods we have applied to social impact assessment questions using Instagram that may be transferrable to other social media platforms and contexts: thematic (manual coding, machine vision, natural language processing/sentiment analysis, statistical analysis), spatial (hotspot mapping, cultural ecosystem modeling), and visual (word clouds, saliency mapping, collage). We conclude with a set of cautions and next steps for the domain.

Parmi les nombreux sous-produits du Web 2.0 figure un large éventail de données provenant d'images et de textes, de contenus de médias sociaux et de plateformes numériques, qui révèlent comment les gens vivent, ce qu'ils font et les questions qui les préoccupent. Ces ensembles de données sont imparfaits et biaisés à bien des égards, mais nombre de leurs lacunes les rendent complémentaires des informations collectées par les sciences sociales à l'aide de méthodes conventionnelles. D'où leur utilité potentielle pour la triangulation dans des contextes décisionnels complexes. Cet article synthétise le travail de trois études de cas menées au Canada pour illustrer certaines des méthodes que nous avons développées et qui pourraient être utiles à d'autres chercheurs en EIS: thématiques (codage, apprentissage automatique, analyse sémantique, association statistique), spatiales (cartographie des points chauds, modélisation du transfert des bénéfices) et visuelles (cartes de saillance, collage).

Entre los muchos subproductos de la Web 2.0 se encuentra una amplia gama de datos de imágenes y texto, contenidos en redes sociales y plataformas digitales, que hablan de cómo vive, qué hace y por qué cuestiones se preocupa la gente. Estos conjuntos de datos son imperfectos y sesgados en muchos sentidos, pero muchos de sus defectos los hacen complementarios a la información recogida por las ciencias sociales con métodos convencionales. De ahí su potencial utilidad para la triangulación en contextos complejos de toma de decisiones. Este artículo sintetiza el trabajo de tres estudios de caso llevados a cabo en Canadá para ilustrar algunos de los métodos que hemos desarrollado y pueden resultar útiles para otros investigadores en EIS: temáticos (codificación, machine learning, análisis semántico, asociación estadística), espaciales (mapeo de puntos críticos, modelización de transferencia de beneficios) y visuales (mapas de saliencia, collage).

Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge.

IMPORTANCE: Biological wastewater treatment relies on complex microbial communities that assimilate nutrients and break down pollutants in the wastewater. Knowledge about the physiology and metabolism of bacteria in wastewater treatment plants (WWTPs) may therefore be used to improve the efficacy and economy of wastewater treatment. Our current knowledge is largely based on 16S rRNA gene amplicon profiling, fluorescence in situ hybridization studies, and predictions based on metagenome-assembled genomes. Bacterial isolates are often required to validate genome-based predictions as they allow researchers to analyze a specific species without interference from other bacteria and with simple bulk measurements. Unfortunately, there are currently very few pure cultures representing the microbes commonly found in WWTPs. To address this, we introduce an isolation strategy that takes advantage of state-of-the-art microbial profiling techniques to uncover suitable growth conditions for key WWTP microbes. We furthermore demonstrate that this information can be used to isolate key organisms representing global WWTPs.

Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina.

We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.

Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample.

The composition of the vaginal microbiota is known to be influenced by various factors and to be associated with several disorders affecting women's health. Although metagenomics is currently a widely used method for studying the human microbiota, it has certain limitations, such as a lack of information on bacterial viability. It is therefore important to use culture-based methods such as culturomics. Here, we used 35 different culture conditions to comprehensively characterize the vaginal bacterial diversity of a single woman's flora. A total of 206 bacterial species, belonging to six phyla (for a little more than half to Firmicutes, followed mainly by Actinobacteria, Bacteroidetes, and Proteobacteria) and 45 families, and 2 fungal species were cultivated. While several species of lactobacilli have been isolated, a wide variety of other bacteria were also separated, including 65 never reported before in vaginal flora, including a new bacterial species, Porphyromonas vaginalis sp. nov. Extensive culture-based methods are essential to establish a comprehensive, evidence-based repertoire of bacterial viability. If combined with molecular methods, they can provide a much more thorough understanding of the vaginal microbiota and fulfil the unknown part of metagenomic studies.

Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria.

The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10-2, 10-6, 10-12), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10-2 and 10-6 dilutions clustered closely while the 10-12 dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.

Sentiment analysis of the Twitter response to Netflix's Our Planet documentary.

The role of nature documentaries in shaping public attitudes and behavior toward conservation and wildlife issues is unclear. We analyzed the emotional content of over 2 million tweets related to Our Planet, a major nature documentary released on Netflix, with dictionary and rule-based automatic sentiment analysis. We also compared the sentiment associated with species mentioned in Our Planet and a set of control species with similar features but not mentioned in the documentary. Tweets were largely negative in sentiment at the time of release of the series. This effect was primarily linked to the highly skewed distributions of retweets and, in particular, to a single negatively valenced and massively retweeted tweet (>150,000 retweets). Species mentioned in Our Planet were associated with more negative sentiment than the control species, and this effect coincided with a short period following the airing of the series. Our results are consistent with a general negativity bias in cultural transmission and document the difficulty of evoking positive sentiment, on social media and elsewhere, in response to environmental problems.

Análisis de sentimientos de la respuesta en Twitter al documental Nuestro Planeta de Netflix Resumen No está claro el papel que tienen los documentales sobre naturaleza en la formación de actitudes públicas y respuestas a los temas de conservación y vida silvestre. Aplicamos un análisis automático de sentimientos basado en reglas y el diccionario al contenido emocional de más de dos millones de tuits relacionados a Nuestro Planeta, un importante documental estrenado en Netflix. También comparamos entre los sentimientos asociados a las especies mencionadas en el documental y un conjunto de especies control con características similares pero que no mencionan en el documental. En general, los tuits contenían sentimientos negativos cuando se estrenó la serie. Relacionamos este efecto a la distribución sesgada de retuits particularmente de un solo tuit negativo con retuits masivos (>150,000). Las especies mencionadas estuvieron asociadas con más sentimientos negativos que las especies control. Este efecto coincidió con un periodo corto después de la emisión de la serie. Nuestros resultados son coherentes con un sesgo generalizado de negatividad en la transmisión cultural y documentan lo difícil que es provocar sentimientos positivos, en redes sociales o en demás sitios, como respuesta a los problemas ambientales.

Achieving a real-time online monitoring system for conservation culturomics.

Environmental monitoring is increasingly shifting toward a set of systems that describe changes in real time. In ecology specifically, a series of challenges have prevented the rollout of real-time monitoring for features such as biodiversity change or ecosystem service provision. Conservation culturomics, a field concerned with interactions between people and nature, is well placed to demonstrate how monitoring might move toward a network of real-time platforms, given its existence exclusively in the digital realm. We examined a set of considerations associated with the development of real-time monitoring platforms for conservation culturomics and introduce a near real-time platform for the Species Awareness Index, a global index of changing biodiversity awareness derived from the rate of change in page views for species on Wikipedia. This platform will update automatically each month, operating in near real time (https://joemillard.shinyapps.io/Real_time_SAI/). There are plans to make the underlying data queryable via an application programing interface independent of the platform. The real-time Species Awareness Index will represent the first real-time and entirely automated conservation culturomic platform and one of the first real-time platforms in the discipline of ecology. Real-time monitoring for culturomics can provide insight into human-nature interactions as they play out in the physical realm and provide a framework for the development of real-time monitoring in ecology. Real-time monitoring metrics can be processed on private virtual machines and hosted on publicly available cloud services. Conservation now needs an online, real-time observatory that can evolve with the structure of the web.

Obtención de un sistema virtual de monitoreo en tiempo real para la culturomía de la conservación Resumen El monitoreo ambiental se enfoca cada vez más en un conjunto de sistemas que describen los cambios en tiempo real. En cuanto a la ecología, una serie de obstáculos ha impedido el despliegue del monitoreo en tiempo real para funciones como el cambio en la biodiversidad o el suministro de servicios ambientales. La culturomía de la conservación, un campo enfocado en las interacciones entre las personas y la naturaleza, es una buena opción para demostrar cómo el monitoreo podría transformarse en una red de plataformas en tiempo real, dado que sólo existe en el ámbito digital. Analizamos una serie de consideraciones asociadas con el desarrollo de plataformas de monitoreo en tiempo real para la culturomía de la conservación e introdujimos una plataforma casi en tiempo real para el Índice de Conciencia de Especies, un índice mundial del cambio en la conciencia sobre la biodiversidad derivado de la tasa de cambio en las visitas a las páginas de Wikipedia de diferentes especies. Esta plataforma se actualizará automáticamente cada mes, por lo que opera casi en tiempo real (https://joemillard.shinyapps.io/Real_time_SAI/). Existen planes para hacer que los datos subyacentes sean consultables por medio de una interfaz de programación de aplicaciones independiente de la plataforma. El Índice de Conciencia de Especies en tiempo real será la primera plataforma de culturomía de la conservación automatizada por completo y en tiempo real, así como una de las primeras plataformas de este tipo para la disciplina de la ecología. El monitoreo en tiempo real de la culturomía puede proporcionar información sobre las interacciones humano-naturaleza conforme se desarrollan en el ámbito físico y también un marco de trabajo para el desarrollo del monitoreo en tiempo real para la ecología. Las medidas del monitoreo en tiempo real pueden procesarse en máquinas virtuales privadas y albergarse en servicios públicos de nubes de almacenamiento. Hoy en día, la conservación necesita un observatorio en línea y en tiempo real que pueda evolucionar con la estructura de la web.

Evaluating global interest in biodiversity and conservation.

The first target of the Convention for Biological Diversity (Aichi target 1) was to increase public awareness of the values of biodiversity and actions needed to conserve it-a key prerequisite for other conservation targets. Monitoring success in achieving this target at a global scale has been difficult; however, increased digitization of human life in recent decades has made it easier to measure people's interests at an unprecedented scale and allows for a more comprehensive evaluation of Aichi target 1 than previously attempted. We used Google search volume data for over a thousand search terms related to different aspects of biodiversity and conservation to evaluate global interest in biodiversity and its conservation. We also investigated the correlation of interest in biodiversity and conservation across countries to variables related to biodiversity, economy, demography, research, education, internet use, and presence of environmental organizations. From 2013 to 2020, global searches for biodiversity components increased, driven mostly by searches for charismatic fauna (59% of searches were for mammal species). Searches for conservation actions, driven mostly by searches for national parks, decreased since 2019, likely due to the COVID-19 pandemic. Economic inequality was negatively correlated with interest in biodiversity and conservation, whereas purchasing power was indirectly positively correlated with higher levels of education and research. Our results suggest partial success toward achieving Aichi target 1 in that interest in biodiversity increased widely, but not for conservation. We suggest that increased outreach and education efforts aimed at neglected aspects of biodiversity and conservation are still needed. Popular topics in biodiversity and conservation could be leveraged to increase awareness of other topics with attention to local socioeconomic contexts.

Evaluación del interés mundial en la biodiversidad y la conservación Resumen La primera meta del Convenio sobre la Diversidad Biológica (Meta 1 de Aichi) era aumentar la conciencia pública sobre los valores de la biodiversidad y las acciones necesarias para conservarla, un requisito previo clave para otras metas de conservación. Ha sido difícil monitorear el éxito en la obtención de esta meta a escala mundial; sin embargo, la creciente digitalización de la vida humana en las últimas décadas ha facilitado la medición de los intereses de la gente a una escala sin precedentes y permite una evaluación más exhaustiva de la Meta 1 de Aichi que la que se había intentado previamente. Utilizamos datos sobre el volumen de búsquedas en Google de más de mil términos relacionados con distintos aspectos de la biodiversidad y la conservación para evaluar el interés mundial en la biodiversidad y su conservación. También investigamos la correlación del interés por la biodiversidad y la conservación en los distintos países con variables relacionadas a la biodiversidad, la economía, la demografía, la investigación, la educación, el uso del internet y la presencia de organizaciones ambientalistas. Las búsquedas mundiales sobre los componentes de la biodiversidad aumentaron de 2013 a 2020, impulsadas sobre todo por búsquedas de especies carismática (el 59% de las búsquedas correspondían a especies de mamíferos). Las búsquedas de acciones de conservación, impulsadas principalmente por búsquedas de parques nacionales, han disminuido desde 2019, probablemente debido a la pandemia de COVID-19. La desigualdad económica se correlacionó negativamente con el interés en la biodiversidad y la conservación, mientras que el poder adquisitivo se correlacionó indirectamente de manera positiva con niveles más altos de educación e investigación. Nuestros resultados sugieren un éxito parcial en la obtención de la Meta 1 de Aichi en el sentido de que aumentó ampliamente el interés por la biodiversidad, pero no por la conservación. Sugerimos que se necesitan mayores esfuerzos de divulgación y educación dirigidos a aspectos desatendidos de la biodiversidad y la conservación. Los temas populares de biodiversidad y conservación podrían aprovecharse para aumentar la conciencia sobre otros temas si se presta atención a los contextos socioeconómicos locales.

Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study.

Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.

Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis.

The novel bacterial strain Marseille-P4005T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed.

A Culturomics-Based Bacterial Synthetic Community for Improving Resilience towards Arsenic and Heavy Metals in the Nutraceutical Plant Mesembryanthemum crystallinum.

Plant-growth-promoting bacteria (PGPB) help plants thrive in polluted environments and increase crops yield using fewer inputs. Therefore, the design of tailored biofertilizers is of the utmost importance. The purpose of this work was to test two different bacterial synthetic communities (SynComs) from the microbiome of Mesembryanthemum crystallinum, a moderate halophyte with cosmetic, pharmaceutical, and nutraceutical applications. The SynComs were composed of specific metal-resistant plant-growth-promoting rhizobacteria and endophytes. In addition, the possibility of modulating the accumulation of nutraceutical substances by the synergetic effect of metal stress and inoculation with selected bacteria was tested. One of the SynComs was isolated on standard tryptone soy agar (TSA), whereas the other was isolated following a culturomics approach. For that, a culture medium based on M. crystallinum biomass, called Mesem Agar (MA), was elaborated. Bacteria of three compartments (rhizosphere soil, root endophytes, and shoot endophytes) were isolated on standard TSA and MA media, stablishing two independent collections. All bacteria were tested for PGP properties, secreted enzymatic activities, and resistance towards As, Cd, Cu, and Zn. The three best bacteria from each collection were selected in order to produce two different consortiums (denominated TSA- and MA-SynComs, respectively), whose effect on plant growth and physiology, metal accumulation, and metabolomics was evaluated. Both SynComs, particularly MA, improved plant growth and physiological parameters under stress by a mixture of As, Cd, Cu, and Zn. Regarding metal accumulation, the concentrations of all metals/metalloids in plant tissues were below the threshold for plant metal toxicity, indicating that this plant is able to thrive in polluted soils when assisted by metal/metalloid-resistant SynComs and could be safely used for pharmaceutical purposes. Initial metabolomics analyses depict changes in plant metabolome upon exposure to metal stress and inoculation, suggesting the possibility of modulating the concentration of high-value metabolites. In addition, the usefulness of both SynComs was tested in a crop plant, namely Medicago sativa (alfalfa). The results demonstrate the effectiveness of these biofertilizers in alfalfa, improving plant growth, physiology, and metal accumulation.

Comparing Vaginal and Endometrial Microbiota Using Culturomics: Proof of Concept.

It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal-cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is not merely a reflection of contamination originating from sampling. Therefore, we investigated to what extent the endometrial microbiome corresponds to that of the vagina, applying culturomics on paired vaginal and endometrial samples. Culturomics could give novel insights into the microbiome of the female genital tract, as it overcomes sequencing-related bias. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy were included. An additional vaginal swab was taken from each participant right before hysteroscopy. Both endometrial biopsies and vaginal swabs were analyzed using our previously described WASPLab-assisted culturomics protocol. In total, 101 bacterial and two fungal species were identified among these 10 patients. Fifty-six species were found in endometrial biopsies and 90 were found in vaginal swabs. On average, 28 % of species were found in both the endometrial biopsy and vaginal swab of a given patient. Of the 56 species found in the endometrial biopsies, 13 were not found in the vaginal swabs. Of the 90 species found in vaginal swabs, 47 were not found in the endometrium. Our culturomics-based approach sheds a different light on the current understanding of the endometrial microbiome. The data suggest the potential existence of a unique endometrial microbiome that is not merely a presentation of cross-contamination derived from sampling. However, we cannot exclude cross-contamination completely. In addition, we observe that the microbiome of the vagina is richer in species than that of the endometrium, which contradicts the current sequence-based literature.