bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcription shifts in gut bacteria shared between mothers and infants
Authors: Vatanen Tommi
Published: September 2024

A portion of strains in the infant gut microbiomes originate from the maternal gut. In the infant gut these bacteria encounter a new metabolic environment that differs from the adult gut, potentially requiring adjustments in their activities. We used community RNA sequencing data (metatranscriptomes) from ten mother-infant dyads participating in the NiPPeR Study to characterize bacterial gene expression shifts following mother-to-infant transmission. Maternally-derived bacterial strains exhibited large scale gene expression shifts following the transmission to the infant gut, with 12,564 activated and 14,844 deactivated gene families. The implicated genes were most numerous and the magnitude shifts greatest in Bacteroides spp. and included genes involved in, for example, carbohydrate utilisation and lysogenic phage activity. Community functions were contrastingly different between mothers and infants on DNA, but not on RNA level; this suggests that bacteria compensated for variations in DNA gene abundance by collectively adjusting gene expression to maintain diverse and stable community activity profiles. Collectively, these data demonstrate environment-dependent, strain-specific shifts in gut bacteria function and underscores the importance of metatranscriptomic analysis in microbiome studies.
Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria is Governed by a Global Transcriptional Regulator NagR
Authors: Arzamasov Aleksandr
Published: September 2024

Bifidobacterium longum subsp. infantis (B. infantis) is a prevalent beneficial bacterium colonizing the human neonatal gut. Decreased abundance of B. infantis contributes to the development of severe acute malnutrition (SAM) in children from the least developing countries. Therapeutic approaches for treating SAM involve using human milk oligosaccharides (HMOs) as dietary additions (prebiotics) to stimulate the growth of B. infantis and confer multiple health benefits to malnourished children. However, the rational selection of HMO-based prebiotics is hampered by the incomplete knowledge of regulatory mechanisms governing HMO utilization in this bacterium. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of genomic loci encoding lacto-N-biose/galacto-N-biose (LNB/GNB), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) utilization pathways in B. infantis. This conjecture was corroborated by transcriptome profiling upon nagR genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated N-acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR effectors. The elucidated regulatory network appears optimally adapted to simultaneous utilization of multiple HMOs, providing a rationale to add HMO mixtures (rather than individual components) into infant formulas to restore B. infantis levels in malnourished children.
A catalogue of small proteins from the global microbiome
Authors: Duan YiQian
Published: September 2024

Small Open Reading Frames (smORFs, operationally defined as those with fewer than 100 codons) are often neglected due to the limitation of computational and experimental methods. Recently, systematic studies have shown that smORFs are widely distributed ecologically and perform diverse functions. However, little is known about the distribution and role of smORFs in the global microbiome. Therefore, we constructed the global microbial smORFs catalogue (GMSC) from 63,410 publicly-available metagenomes across 72 distinct habitats and 87,920 high-quality isolated microbial genomes. GMSC (available at https://gmsc.big-data-biology.org/) contains 964,970,496 non-redundant smORFs, the majority of which are novel. We found that archaea harbor more small proteins than bacteria (as a fraction of their genomes). To enable the use of this resource, we provide a tool called GMSC-mapper that can identify and annotate reliable smORFs from microbial genomes and metagenomes. The resource shows an immense and underexplored diversity of smORFs and can be used to research the presence, distribution, and role of smORFs at the global scale.
Microbiome Science for Everyone: MVIF season 1&2
Authors: Taylor Shanya
Published: September 2024

The Microbiome Virtual International Forum (MVIF) is a substitute for multi-day microbiome conferences. MVIF was created by microbiome scientists with intent to be free, beneficial, and convenient for scientists all over the world, no matter their career stage. The MVIF creators are hoping to make the event as productive as possible. Therefore, in this NSURP2023 project (https://nsurp.org/), my aim was to compare MVIF Season 1 and MVIF Season 2 by compiling speakers’ information from https://www.microbiome-vif.org/en-US/-/past-events and documenting it in a Google Sheet. I hypothesized that there would be a few differences between the seasons in some aspects of the past MVIF events. The speakers’ metadata was analyzed using Python libraires: pandas, numpy and matplotlib. The results showed that there were a total of 142 speakers with 53% being females and the remaining 47% being males. For both seasons, most of the speakers’ affiliated locations were the USA and European countries and their talks focused on the human gut and bioinformatics. I was able to see a difference between the two seasons: Season 1 had a total of 82 speakers (with consequently a higher number of talks) whereas Season 2 had 60 speakers. Although season 1 had more diverse microbiome topics, in Season 2 there’s a slight increase in non-human microbiome topics, such as water microbiome. From September, there will be a new season with an effort to amplify more diverse voices of microbiome science.
Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer
Authors: Niño Jorge L Galeano
Published: September 2024

The tumour-associated microbiota is an intrinsic component of the tumour microenvironment across human cancer types. Intratumoral host–microbiota studies have so far largely relied on bulk tissue analysis, which obscures the spatial distribution and localized effect of the microbiota within tumours. Here, by applying in situ spatial-profiling technologies and single-cell RNA sequencing to oral squamous cell carcinoma and colorectal cancer, we reveal spatial, cellular and molecular host–microbe interactions. We adapted 10x Visium spatial transcriptomics to determine the identity and in situ location of intratumoral microbial communities within patient tissues. Using GeoMx digital spatial profiling, we show that bacterial communities populate microniches that are less vascularized, highly immuno suppressive and associated with malignant cells with lower levels of Ki-67 as compared to bacteria-negative tumour regions. We developed a single-cell RNA-sequencing method that we name INVADEseq (invasion–adhesion-directed expression sequencing) and, by applying this to patient tumours, identify cell-associated bacteria and the host cells with which they interact, as well as uncovering alterations in transcriptional pathways that are involved in inflammation, metastasis, cell dormancy and DNA repair. Through functional studies, we show that cancer cells that are infected with bacteria invade their surrounding environment as single cells and recruit myeloid cells to bacterial regions. Collectively, our data reveal that the distribution of the microbiota within a tumour is not random; instead, it is highly organized in microniches with immune and epithelial cell functions that promote cancer progression.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.11.07.515285v1
Ethical and rigorous human microbiome science requires radical interdisciplinary co-laboration
Authors: Daele Wim van
Published: September 2024

Current human microbiome science is still marked by a European and North American bias with many important ethical implications on the horizon. In addition, the limited research on other understudied populations is not without its ethical quandaries either. In this presentation, I discuss and clarify these ethical issues by disentangling these into 3 main subsets: European and North American bias, cultural insensitivity, and lack of meaningful collaboration and inclusion. Thereafter, I propose an overall approach to solving these quandaries by introducing the notion of radical interdisciplinary co-laboration, in which different academic and non-academic stakeholders mediate their knowledges and labor together in studying human microbiomes. I will elicit how the proposed approach will render microbiome science more ethical and at the same time render the very science of microbiomes more precise and rigorous.
Molecular mechanisms of microbial modulation of skin homeostasis
Authors: Oh Julia
Published: September 2024

The human skin harbors an abundant microbial ecosystem with bidirectional metabolic exchanges supporting symbiotic and commensal functions. Metagenomic analyses of the diverse skin sites in healthy humans demonstrate that contrasting forces of the skin’s biogeography and individual characteristics shape the skin microbiome and the dynamics of its bacteria, fungi, and viruses. However, we have shown that shifts in the ecological properties of the skin microbiome are significantly associated with aging, skin disease, disease severity, and monogenic skin and immune disorders. We have used a variety of computational and functional approaches, including metagenomics, CRISPRi screening, organoid platforms, transcriptomic and spatial transcriptomics, and other technologies to probe genetic and functional diversity of the skin microbiome.
Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life
Authors: Glendinning Laura
Published: September 2024

Microbiota transplantation studies in chickens represent a fascinating opportunity to study the impact of early-life microbiota manipulation on important phenotypes such as pathogen resistance and nutrition. When chicks are raised by a maternal hen, they quickly develop a gastrointestinal microbiota that is similar to their mother. However, commercially-raised chicks have no direct contact with maternal hens or their faeces. They subsequently develop a less-diverse microbiota that is seeded from their environment. By delivering microbiota transplants from chickens with a desired phenotype to chicks raised without maternal contact we can define the trajectory of their microbiota development. This allows us to examine the impact of the transplanted microbiota on the development of desired phenotypes. However, studies have shown varying success when attempting to conduct microbiota transplants in chickens, potentially due to the variability of techniques used. We investigated whether it was possible to transplant the caecal microbiota between 40 week old adult chickens and freshly hatched chicks from a different chicken breed. Caecal contents were collected from the adult birds and within 30 minutes were administered orally to chicks. The microbiota of treated and control chicks was characterised via 16S rRNA gene sequencing at 1, 2, 3, 4, and 7 days post-hatch. At all timepoints, the microbiota of treated chicks was significantly different in composition and richer and more diverse than control birds. Transplantation clearly changed the trajectory of the treated birds so that they developed a microbiota which was far more similar to the donor birds than the control chicks. The most notable taxonomic difference between control and treated birds was the abundance of the phylum Bacteroidota. This phylum was present in high relative abundance in the donor samples (38%) and also in the treated samples (day 7: 41%). However, it was almost completely absent from the control birds (Day7: 0.02%). We therefore demonstrate that our technique is highly effective at transplanting the caecal microbiota between adult donors and chicks from a different chicken breed. This technique could be further used to study the role of the microbiota in chicken breeds with differing phenotypes.

Link to OA paper: https://www.sciencedirect.com/science/article/pii/S0032579121006453
Dynamic changes in small intestinal stoma microbiota
Authors: Yilmaz Bahtiyar
Published: September 2024

Ileum has a distinct microbiota but human studies investigating its composition and function have been limited by the inaccessibility of the ileum without purging and/or deep intubation. In this recently published study, we investigated inherent instability, temporal dynamics, and the contribution of fed to the otherwise inaccessible small and large intestines. Longitudinal samples from the ileum before and after stoma formation indicated that ileostoma microbiotas represented that of the intact small intestine. Ileal and colonic stoma microbiotas were confirmed as distinct, and two types of instability: i) inter-digestive purging followed by the rapid postprandial blooming of bacterial biomass and sub-strain appearance and ii) disappearance within individual taxa after feeding. In contrast to the relative stability of colonic microbiota, small intestinal microbiota biomass and its sub-strain composition can be highly dynamic.

Link to OA paper: https://www.sciencedirect.com/science/article/pii/S1931312822005157?dgcid=coauthor
Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant
Authors: Heidrich Vitor
Published: September 2024

Background Allogeneic hematopoietic stem-cell transplant (allo-HSCT) is a potentially curative therapy for several hematological disorders. Before stem-cell infusion, recipients undergo a conditioning regimen with chemo/radiotherapy and immunosuppressants, requiring the use of antibiotics to treat and prevent infections. This regimen promotes drastic alterations in the recipient′s microbiotas, including the oral microbiota, which have been associated with allo-HSCT complications and poor outcomes. However, long-term longitudinal studies on the oral microbiota of allo-HSCT recipients are scarce and disregard the existence of distinct microbiotas within the oral cavity. Here, we used 16S rRNA gene sequencing to characterize the microbiota dynamics (during and after allo-HSCT) of 31 allo-HSCT recipients at 3 oral sites (gingival crevicular fluid, oral mucosa, and supragingival biofilm). Results Analysis of the oral microbiota dynamics during allo-HSCT revealed a significant decline in bacterial diversity and major shifts in microbiota composition in all oral sites, including blooms of potentially pathogenic genera. These blooms in some cases preceded respiratory infections caused by the blooming genera. We also noticed that differences in microbiota diversity and composition between oral sites were lost during allo-HSCT. Overall, oral microbiotas returned to their preconditioning state after engraftment. However, the ability to recover the initial bacterial composition varied between patients. After stratifying patients based on their ability to recover their preconditioning microbiota composition, we found that recovery of the oral mucosa microbiota composition was not associated with antibiotic usage but was associated with higher preconditioning diversity and earlier reconstitution of normal leukocyte counts. Most notably, oral mucosa microbiota composition recovery was an independent biomarker of better allo-HSCT outcomes. Conclusion We observed clear patterns of microbiota dysbiosis in all three oral sites during allo-HSCT, however each oral site responded differently to the perturbations associated with allo-HSCT. Oral microbiota injury and recovery patterns were associated with allo-HSCT complications and outcomes. This study highlights the potential clinical impact of the oral microbiota in the allo-HSCT setting and the clinical value of tracking oral microbiota changes during allo-HSCT.

Link to OA paper: https://www.medrxiv.org/content/10.1101/2022.11.18.22282520v1
Functional screens of barcoded expression libraries uncover new gene functions in carbon utilization among gut Bacteroidales
Authors: Huang Yolanda Y.
Published: September 2024

A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate gene discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut bacterial genes have been performed in an aerobic host and included a small number of conditions. To address these challenges, we developed a strategy to barcode expression libraries for high-throughput interrogation of gene functions in competitive fitness assays. We demonstrate the power of this approach to uncover novel phenotypes for uncharacterized genes using pooled libraries constructed from a diverse set of gut Bacteroidales expressed in Bacteroides thetaiotaomicron. We identified new roles in carbohydrate metabolism for nine proteins, including enzymes, transporters, a regulator, and hypothetical proteins from mobile genetic elements. This approach can be readily applied to other organisms and additional phenotypic assays.
Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.10.05.510937v1
The Human Microbiome in Precision Medicine
Authors: Gilbert Jack
Published: September 2024

The human microbiome is a high dimensional and dynamic part of our physiology that plays a key role in managing health and individualized responses to diet and medicine. The immune system controls our interaction with the microbial world, and the microbial communities in our bodies are central to modulating the immune response. Changes in the human microbiome and their metabolism have substantial influence on atopy, neurological disorders, metabolic disorders, and a range of complex conditions and disease states. Diet is incredibly important in shaping human health and the microbiome, altering both composition and metabolic activity, resulting in changes in immune, endocrine, and neurological systems. Microbiome-Wide Association Studies (MWAS) combined with novel quantitative multi-omic approaches are enabling us to use AI techniques to determine personalized responses to nutrition that drive diseases states and treatment efficacy. Through these innovations, we are finally realizing the paradigm of precision medicine for facilitating patient care.
Gut microorganisms and their genes are associated with cognition and neuroanatomy in children
Authors: Bonham Kevin Scott
Published: September 2024

The gastrointestinal tract, its resident microorganisms, and the central nervous system are connected by biochemical signaling, also known as the ”microbiome-gut-brain-axis.” Both the human brain and the gut microbiome have critical developmental windows in the first years of life, raising the possibility that their development is co-occurring and likely co-dependent. Emerging evidence implicates gut microorganisms and microbiota composition in cognitive outcomes and neurodevelopmental disorders (e.g., autism and anxiety), but the influence of gut microbial metabolism on typical neurodevelopment has not been explored in detail. We investigated the relationship of the microbiome with the neuroanatomy and cognitive function of 361 healthy children, demon- strating that differences in gut microbial taxa and gene functions are associated with overall cognitive function and with differences in the size of multiple brain regions. Using a combination of multivariate linear and machine learning (ML) models, we showed that many species, including Gordonibacter pamelae and Blautia wexlerae, were significantly associated with higher cognitive function, while some species such as Ruminococcus gnavus were more commonly found in children with low cognitive scores after controlling for sociodemographic factors. Microbial genes for enzymes involved in the metabolism of neuroactive compounds, particularly short-chain fatty acids such as acetate and propionate, were also associated with cognitive function. In addition, ML models were able to use microbial taxa to predict the volume of brain regions, and many taxa that were identified as important in predicting cognitive function also dominated the feature importance metric for individual brain regions. For example, B. wexlerae was the most important species in models predicting the size of the parahippocampal region in both the left and right hemispheres, while several species from the phylum Bacteroidetes, including GABA-producing B. ovatus, were important for predicting the size of the left accumbens area, but not the right. These findings provide potential biomarkers of neurocognition and brain development and may lead to the future development of targets for early detection and early intervention.

Link to OA paper: https://doi.org/10.1101/2020.02.13.944181
Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome
Authors: Johnson Kelsey
Published: September 2024

Human milk is a complex mix of nutritional and bioactive components that provide complete nutrition for the infant. However, we lack a systematic knowledge of the factors shaping milk composition and how milk variation influences infant health. Here, we used multi-omic profiling to characterize interactions between maternal genetics, milk gene expression, milk composition, and the infant fecal microbiome in 242 exclusively breastfeeding mother-infant pairs. We identified 487 genetic loci harboring variants associated with milk cell gene expression unique to the lactating mammary gland. Genetic effects on milk gene expression included genes with roles in the biosynthesis of specific human milk oligosaccharides (HMO), including a genetic variant that increases the expression of the gene GCNT3 in milk and is also associated with increased concentration of the HMO FLNH. Integrative analyses uncovered connections between milk gene expression and infant gut microbiome, including an association between the expression of inflammation-related genes with IL-6 concentration in milk and the abundance of Bifidobacteria in the infant gut. Our results show how an improved understanding of the genetics and genomics of human milk connects lactation biology with maternal and infant health.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2023.01.24.525211v1
Gene Editing in Agriculture
Authors: Chapman Tracey
Published: September 2024

Powered by best-in-class technology, Pairwise tackles the challenges that our food and agricultural system face to achieve our goal of building a healthier world through better fruits and vegetables. Here, we describe work done by the Pairwise pipeline achieving agronomic improvements in corn and blackberry. In corn, we use DNA base editing to demonstrate a tunable increase in kernel row number, while in blackberry we use gene editing to achieve a compact structure and early flowering plants. Taken together, this work shows the power of gene editing and the Pairwise product pipeline to positively impact crop performance across various species.
Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88–/– Mice
Authors: Udayan Sreeram
Published: September 2024

In healthy hosts the gut microbiota is restricted to gut tissues by several barriers some of which require MyD88-dependent innate immune sensor pathways. Nevertheless, some gut taxa have been reported to disseminate to systemic tissues. However, the extent to which this normally occurs during homeostasis in healthy organisms is still unknown. In this study, we recovered viable gut bacteria from systemic tissues of healthy wild type (WT) and MyD88−/− mice. Shotgun metagenomic-sequencing revealed a marked increase in the relative abundance of L. johnsonii in intestinal tissues of MyD88−/− mice compared to WT mice. Lactobacillus johnsonii was detected most frequently from multiple systemic tissues and at higher levels in MyD88−/− mice compared to WT mice. Viable L. johnsonii strains were recovered from different cell types sorted from intestinal and systemic tissues of WT and MyD88−/− mice. L. johnsonii could persist in dendritic cells and may represent murine immunomodulatory endosymbionts.

Link to OA paper: https://www.tandfonline.com/doi/full/10.1080/19490976.2021.2007743
Detailed Social Network Interactions and Gut Microbiome Strain-Sharing Within Isolated Honduras Villages
Authors: Pullman Jackson
Published: September 2024

When humans assemble into face-to-face social networks, they create an extended environment that permits exposure to the microbiome of other members of a population. Social network interactions may thereby also shape the composition and diversity of the microbiome at individual and population levels. Here, we use comprehensive social network and detailed microbiome sequencing data in 1,098 adults across 9 isolated villages in Honduras to investigate the relationship between social network structure and microbiome composition. Using both species-level and strain-level data, we show that microbial sharing occurs between many relationship types, notably including non-familial and non-household connections. Using strain-sharing data alone, we can confidently predict a wide variety of relationship types (AUC  0.73). This strain-level sharing extends to second-degree social connections in a network, suggesting the importance of the extended network with respect to microbiome composition. We also observe that socially central individuals are more microbially similar to the overall village than those on the social periphery. Finally, we observe that clusters of microbiome species and strains occur within clusters of people in the village social networks, providing the social niches in which microbiome biology and phenotypic impact are manifested.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2023.04.06.535875v1
Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases
Authors: Zhao Liping
Published: September 2024

Gut microbiota may work as an essential organ and its members interact closely with each other and form a higher-level organization called guilds. How such guild-level structure supports the gut microbiota to stably provide essential health-relevant functions to the host remains elusive. With high quality metagenome-assembled genomes as network nodes, here we identified a core microbiome signature made up of two robust competing guilds that together correlate with a wide range of host health conditions. Genomes in these two guilds kept their ecological relationship unchanged despite experiencing profound abundance changes during a 3-month high fiber intervention and 1-year follow-up in patients with type 2 diabetes. The genomes of one guild harbored more genes for plant polysaccharide degradation and butyrate production, while the other guild had more genes for virulence or antibiotic resistance. A Random Forest regression model showed that the abundance distributions of these genomes were associated with 41 out of 43 bio-clinical parameters in the study cohort. With these genomes as reference, Random Forest modeling successfully classified case and control of 8 chronic diseases in 12 independent metagenomic datasets from 1,816 participants across ethnicity and geography. This core microbiome signature49 may facilitate ecological management of chronic diseases.
Of microbiomes and research integrity: scientific misconduct in microbiology and beyond
Authors: Bik Elisabeth
Published: September 2024

Science builds upon science. Even after peer-review and publication, science papers could still contain images or other data of concern. If not addressed post-publication, papers containing incorrect or even falsified data could lead to wasted time and money spent by other researchers trying to reproduce those results. Several high-profile science misconduct cases have been described, but many more cases remain undetected. Elisabeth Bik is an image forensics detective with a microbiology background, who left her paid job in industry to search for and report biomedical articles that contain errors or data of concern. She has done a systematic scan of 20,000 papers in 40 journals and found that about 4% of these contained inappropriately duplicated images. In her talk she will discuss her career shift from working in academia and industry on microbiome research to her present work on inappropriately duplicated images and other examples of research misconduct. In addition, she will show how to report scientific papers of concern, and how journals and institutions handle such allegations.
A guided tour into genomic contamination detection
Authors: Cornet Luc
Published: September 2024

Nowadays, genomes constitute the basis of many research endeavors. This is especially true since the decrease of sequencing cost has led to an explosion of the number of genomes in public repositories. Estimating the amount of contamination, i.e. the inclusion of unwanted DNA in genomic materials, of this deluge of data has become a field in itself, with numerous algorithms now available and an increasing rate of publication over the years. As newly released tools do not simply replace older ones, but have their own scope, it becomes difficult for scientists to efficiently determine which tool to use in their study. Recently, we have published an overview of the main characteristics and applicability of 18 algorithms dedicated to the estimation of genomic contamination. For instance, the conceptual differences between database-free tools and those associated with a reference database have an effect on detection sensitivity, as do the difference between genomewide and marker-based methods. Beyond this typology of tools, we present here a new analysis designed to compare algorithms on a large simulated dataset derived from empirical data. This protocol, dubbed CRACOT for CRitical Assessment of COntamination detection at multiple Taxonomic levels, reveals both under- and over-detection by even the most commonly used algorithms, with simulated contamination events ranging from inter-phylum to inter-species.
Functional and evolutionary characterization of unknown genes from uncultivated taxa
Authors: Río Álvaro Rodríguez del
Published: September 2024

Over the last decades, the sequencing of environmental DNA by metagenomics has provided the genomes of thousands of uncultivated bacterial and archaeal lineages, revealing an enormous amount of previously unknown genes. Even though recent studies have highlighted the apparent importance of these novel genes, their overall significance is still largely unexplored. Here, we applied a comprehensive comparative genomics approach to identify high-quality novel protein families exclusive from uncultivated species, and characterized them from a functional, ecological and evolutionary point of view. For such a purpose, we computed protein families from a large multi-habitat metagenomic dataset covering 400M genes from 170k genomes spanning the prokaryotic phylogeny. We then applied strict quality and novelty filters to avoid incomplete genes, assembling artifacts, distant homologs and potential pseudogenes. This led us to uncovering 400K high-quality gene families exclusive from uncultivated taxa, twice the number of gene families in reference databases like EggNOG. These high-quality novel gene families are widespread within and across habitats, indicating their ecological value. They also spread out across the microbial phylogeny and are notably overrepresented in recently discovered taxa. Most remarkably, we found that 980 previously neglected protein families can accurately distinguish entire uncultivated phyla, classes and orders, likely representing synapomorphic traits. We inferred the putative functional roles of the high-quality novel gene families by reconstructing their genomic neighborhood and estimating their degree of functional context conservation. 18% of the novel protein families are present in phylogenetically conserved operon regions, in some cases involving key metabolic genes, suggesting they may take part in central microbial processes. In order to facilitate the characterization of novel gene families in relevant genomic contexts, we developed http://novelgenefamilies.compgenomics.org, which allows to browse and visualize the genomic neighbors of any of our novel gene family predictions. Overall, our work provides a global phylogenomic analysis of the largely uncharted repertoire of unique genes from uncultured prokaryotes, serving as a base resource for further investigations on their functional and ecological roles.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.01.26.477801v1
A Microbiome Restoration Strategy Modulates the Gut Microbiome and Metabolic Markers in Healthy Adults
Authors: Li Fuyong
Published: September 2024

The dramatic increase of chronic diseases in industrialized societies might be driven in part by a disruption of gut microbiome composition and function (e.g., reduced fiber fermentation) and impaired intestinal barrier integrity. We developed a microbiome restoration strategy based on a diet that resembles key aspects of a non-industrialized diet (Non-Ind) and a probiotic Limosilactobacillus reuteri (a species rarely found in microbiome from industrialized populations). Using a randomized controlled pilot study, 30 participants consumed either the Non-Ind diet or their usual diet in a crossover fashion for three weeks each. Participants were also divided into three groups and consumed either a single dose of one of two Lm. reuteri strains or a placebo on day four of each diet period. The Non-Ind diet enhanced the temporal persistence of one of the Lm. reuteri strains, but had no measurable effects on microbiome and host. In contrast, the Non-Ind diet shifted overall fecal microbiome composition (R2=0.015, p=0.001; ADONIS), and significantly altered 56% of Amplicon Sequence Variants obtained from 16S dataset (FDR lower than 0.05), 22% of species-level genome bins, and 21% of metabolic pathways obtained from metagenomic dataset (FDR lower than 0.05). Bacteria fermentation was enhanced, exhibited by increased concentration of total fecal short-chain fatty acids (+10.7%, p=0.03) and reduced fecal pH (-3.8%, p=0.002). Furthermore, we observed reductions in six chronic disease risk markers (all p lower than 0.01): total cholesterol (-14.1%), low-density lipoprotein cholesterol (-16.8%), high-density lipoprotein (HDL) cholesterol (-11.3%), non-HDL cholesterol (-15.2%), glucose (-6.3%), and C-reactive protein (-14.2%). The diet also reduced fecal calprotectin (-21.0%, p=0.002) and zonulin levels (-14.9%, p=0.025) that are markers of gut inflammation and impaired barrier functions, respectively. Our study demonstrates pronounced beneficial effects of a microbiome restoration strategy based on the Non-Ind diet on metabolic markers of health. The findings provide valuable information for improving human health in modern societies. Ongoing analyses are exploring the mechanistic links between diet-induced changes in the gut microbiome and the physiological effects on the host.
A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
Authors: Sim Choon Kiat
Published: September 2024

Background: The human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically present. When these bacteria are present at very low levels, they are often undetectable in hospital surveillance cultures, known as occult or subclinical colonization. Through the use of antibiotics, these subclinical pathogens can increase to sufficiently high levels to become detectable, in a process called outgrowth. However, little is known about the interaction between gut microbiota and Enterobacteriaceae during occult colonization and outgrowth. Results: We developed a clinically-relevant mouse model for studying occult colonization. Conventional wild-type mice without antibiotic pre-treatment were exposed to K. pneumoniae but rapidly tested negative for colonization. This occult colonization was found to perturb the microbiome as detected by both 16S rRNA amplicon and shotgun metagenomic sequencing. Outgrowth of occult K. pneumoniae was induced either by a four-antibiotic cocktail or by individual receipt of ampicillin, vancomycin or azithromycin, which all reduced overall microbial diversity. Notably, vancomycin was shown to trigger K. pneumoniae outgrowth in only a subset of exposed animals (outgrowth-susceptible). To identify factors that underlie outgrowth susceptibility, we analyzed microbiome-encoded gene functions and were able to classify outgrowth-susceptible microbiomes using pathways associated with mRNA stability. Lastly, an evolutionary approach illuminated the importance of xylose metabolism in K. pneumoniae colonization, supporting xylose abundance as a second susceptibility indicator. We showed that our model is generalizable to other pathogens, including carbapenem-resistant Escherichia coli and Enterobacter cloacae. Conclusions: Our modeling of occult colonization and outgrowth could help the development of strategies to mitigate the risk of subsequent infection and transmission in medical facilities and the wider community. This study suggests that microbiota mRNA and small-molecule metabolites may be used to predict outgrowth-susceptibility.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2021.02.24.432587v1
Quantification of gut bacterial strains following fecal transplantation
Authors: Aggarwala Varun
Published: September 2024

Fecal Microbiota Transplantation (FMT) while successful, lacks a quantitative identification of the discrete bacterial strains that stably engraft in recipients, and their association with clinical outcomes. Using the largest collection of more than 1,000 unique bacterial strains cultured from a combination of 22 FMT donors and recipients with recurrent Clostridioides difficile infection (rCDI), we develop an approach Strainer for detection and tracking of bacterial strains from metagenomic sequencing data. On application to 13 FMT interventions, we detect stable and high engraftment of 71% of microbiota strains in recipients at even 5-years post-transplant, a remarkably durable therapeutic from a single administration. Although ~80% of the original pre-FMT recipient strains were eliminated by the FMT, those strains that remain persist even 5 years later, along with newer strains acquired from the environment. The precise quantification of donor bacterial strain engraftment in recipients independently explained (precision 100%, recall 95%) the clinical outcomes of relapse or success after both initial and repeat-FMT. We next apply this to the largest successful FMT trial for patients with Ulcerative Colitis (FOCUS study), and found both overall and specific high engraftment of certain bacterial strains and species in patients that achieved the primary endpoint of steroid-free clinical remission with endoscopic remission or response. We provide a list of bacterial species and strains that are present in multiple donors and consistently engraft in recipients over time, for use in Live Biotherapeutic Products (LBP) as a safer alternative to FMT. Our framework can enable the systematic evaluation of different FMT and LBP study designs by quantification of strain engraftment in recipients.
THE IMAGE OF PORTHGENNA TOWER IN THE NOVEL OF W. COLLINS «THE DEAD SECRET»
Authors: SHABUNYA J.
Published: September 2024

The article deals with the image of Porthgenna Tower in the novel “The Dead Secret” (1856) by the English writer and playwright W. Collins. It notes the influence of the Gothic tradition on the work of W. Collins and the description of the main setting. The article describes the importance of the material world, nature and symbolism, which give tension and dramatic effect to the narrative. It reveals the features of the author’s approach to creating an atmosphere of mystery when describing the tower. It analyzes the artistic devices, techniques, and motifs in the novel “The Dead Secret” that create the image of the tower.
CULTURAL CODES IN THE EXPRESSION OF NATIONAL IDENTITY IN THE EPISODE OF BELARUS ON THE BORDER OF THE XX-XXI CENTURIES
Authors: DUKTAVA L.
Published: September 2024

The purpose of this article is to reveal the features of the national worldview, noted in the epic works of Belarusian literature at the turn of the 20th – 21st centuries, in relation to the issue of national identity, when demonstrating which writers turn to cultural codes. When analyzing the views of researchers on the problem of national identity, it is advisable to highlight three aspects: determining the characteristics of the national character (answering the questions “who are we?”, “what are we?”); space-time continuum of the artistic picture of the world (answering the questions “where are we?”, “where are we from?”, “where are we going?”); cultural meanings, translated using cultural codes, when considering the dyads “us – them”, “us – alien” (the answer to the question “who are we with?”). The features of the representation of cultural codes in the epic works of modern Belarusian literature are determined in conjunction with consideration of the issue of national identity.
VICONYMS OF BELARUS AND FRANCE, REFLECTING THE PHYSICAL AND GEOGRAPHICAL FEATURES OF THE AREAS
Authors: DARAFEYENKA M.
Published: September 2024

The article reflects the results of a comparative study of viconyms that reflect the physical and geographical features of the area. The main thematic groups have been identified, including the names of this variety in the subsystems of intravillage names in Belarus and France: “Landscape elements”, “Flora”, “Functional specialization”, “Quality of the object and area”, as well as the quantitative relationships of these groups. Motivating units common to the two national onomastic subsystems are identified. The eponymous and nationally-specific subgroups of names, nominative features characteristic of the analyzed category of names have been established. It has been determined that for this type of viconyms they are characterized as typologically similar (similar name groups, partial coincidence of the structure of the periphery of the semantic field, a certain number of common motivating words used in two subsystems to form names), as well as nationally specific features (different nominative priorities and discrepancies in the structuring of space in viconymy, a significant quantitative discrepancy in the ratio of structural components of the semantic field, the presence of thematic varieties of viconyms characteristic of only one of the subsystems).
Study Gaps in Leadership Styles and Employees Performance in Public Sectors: A Review of Literature
Authors: Hailu Redie Bezabih , Verrier Derek
Published: September 2024

Purpose – The paper aims to examine the relationship of leadership styles and employees job performance in public sectors and to identify study gaps in the areaDesign/methodology/approach – The paper used exploratory study approach and reviewed literatures related to this study. The data used for study was generated from secondary sources of articles, books and review papers.Findings – The paper provides empirical insights about how leadership styles have relations and impacts on employees’ performance and the practice of public service leadership in different contexts and nations.Research limitations/implications – This study used only qualitative method and data were gained from only secondary sources. This may cause generalizability limitations.Practical implications – The paper has significant implication for researchers, role players of public sectors leaders and experts working under the supervision of leaders or managers.Originality/value – This paper is original and own effort of the researcher.
Motivasi kerja islam dalam memediasi hubungan human relation dan beban kerja terhadap kinerja karyawan PT. Metinca Prima Industrial Works Salatiga
Authors: Rahayu Septyana , Pratama Abdul Aziz Nugraha
Published: September 2024

This research aims to analyze and determine the influence of human relations and workload on employee performance, mediated by Islamic work motivation. The method used in this research is quantitative, with primary data obtained from the results of questionnaires distributed and filled in by PT employees. Metinca Prima Industrial Works Salatiga is as many as 118. The data analysis techniques used are path analysis and the Sobel test. The research results show that human relations and Islamic work motivation have a positive and significant effect on performance, while workload has an insignificant positive effect. Workload and human relations positively and significantly affect Islamic work motivation. Islamic work motivation cannot mediate the relationship between human relations and workload on performance.
The Presence of Absence
Authors: Rogers Katina L.
Published: September 2024

The Presence of Absence: Meditations on the Unsayable in Writing is about writers navigating the unspeakable through image, sound, and structure. Each chapter focuses on a specific text, exploring the ways that four writers look to visual and auditory materials and metaphors as passageways to understanding and expressing the ineffable qualities of relationships, identity, and grief. Through gorgeously slow and close readings, Rogers explores absence and excess, fragmentation and translation, and — above all — the push and pull between presence and absence, with absence carrying as much significance as presence (and sometimes more).

The Presence of Absence crosses languages and disciplines, working in French and English across poetry, photography, history, and literary theory. Through investigations of Nox by Anne Carson, Quelque chose noir by Jacques Roubaud, Wayward Lives, Beautiful Experiments by Saidiya Hartman, and Le livre des questions by Edmond Jabès, Rogers explores various truths — about loss but also about knowledge, beauty, even higher education — that are difficult to articulate and yet resonate deeply with lived experience.
Impact of agricultural intervention on socio-economic development of farmers: Evidence from regression discontinuity design
Authors:   Saint Paul Academy, Pagador Romy Jake , Peñas Anthony ,   Camarines Sur Institute of Science and Technology Inc., Obias Cezar ,   Partido State University, Onsay Emmanuel ,   Partido State University
Published: September 2024

The contribution of agriculture in the socio-economic development is undeniable and is truly an important part of the Philippine economy. It is also a major source of livelihood and employment of most Filipinos especially in the rural areas. The general intent of this study is to evaluate the impact of the government agricultural intervention on selected upland communities in Goa, Camarines Sur especially on the far-flung barangays of the municipality using Regression Discontinuity Design. This study assessed the socio-economic and poverty status of the local farmers through the agricultural interventions received. The results showed that the distribution of seeds, fertilizers and cash assistance to the upland farmers could improve the overall outputs of the farmers, which can help alleviate their lives. Similarly, the agricultural interventions of the government have great and positive impact to alleviate poverty and improve the quality of life of the local farmers. However, irrigation and farm-to-market roads need to be prioritized to ensure that agricultural production output increase.