bluuebunny/crossref_metadata_2025 huggingface dataset:
Viroid-like colonists of human microbiomes
Authors: Zheludev Ivan
Published: September 2024

Here, we describe the “Obelisks,” a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. “Obelisks” share several properties: (i) apparently circular RNA about 1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the “Oblins”. We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in about 7% of analysed stool metatranscriptomes (29/440) and in about 50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over 300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1
The infant gut commensal Bacteroides dorei presents a generalized transcriptional response to various Human Milk Oligosaccharides
Authors: Kijner Sivan
Published: September 2024

Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being the third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focused on Bifidobacterium species that harbor many glycoside hydrolases (GHs) tailored to break the carbon bonds in HMO molecules. However, there are additional microbes in the infant gut, such as Bacteroides species, with increasing evidence that they, too, are able to break-down HMOs. To study the unbiased impact of breastfeeding on the infant gut microbiome, we need to investigate the underlying mechanisms of HMO utilization by all members of the infant gut. Here, we developed an optimized system for isolating Bacteroides strains from infant stool samples. We then examined the HMO utilization capacity of multiple Bacteroides isolates by performing growth curves on six common HMOs (2’-FL, DFL, 3’-SL, 6’-SL, LNT, LNnT). Isolates often displayed similar growth characteristics on similarly-structured HMOs, like sialylated or fucosylated sugars. We identified variation in HMO utilization across multiple strains of the same species, and chose to focus here on a Bacteroides dorei isolate that was able to utilize the test HMOs. We performed RNA sequencing on B. dorei cultures, comparing the transcriptional profile in minimal media supplemented with glucose or HMOs. We showed that B. dorei employs an extensive metabolic response to HMOs. Surprisingly, there was no clear up-regulation for most GH families previously known to break-down HMOs, possibly because they were almost exclusively described in Bifidobacterium species. Instead, B. dorei exhibits a generalized response to HMOs, markedly up-regulating several shared GH families across all conditions. Within each GH family, B. dorei displays a consistent pattern of up-regulation of some genes with down-regulation of the others. This response pattern to HMOs has yet to be described in other commensals of the infant gut. Our work highlights the importance of expanding the HMO-microbiome studies beyond Bifidobacterium species, sheds light on the differences across Bacteroides strains in terms of HMO utilization, and paves the way to understanding the mechanisms enabling Bacteroides HMO utilization.
Unlocking microbial activity from complex samples
Authors: Soffer Nitzan
Published: September 2024

The Ribo-Zero Plus Microbiome Depletion Kit offers an RNA-to-analysis workflow solution for metatranscriptomic research. The Ribo-Zero Plus Microbiome depletion probe sets reduce unwanted rRNA reads from stool and other complex samples therefore increasing RNA reads of interest. In addition, the compli­mentary analysis software democratizes this method for both experienced and new microbiome users. The focus on analyzing high-value portions of the transcriptome allows deeper insight into active gene function in the microbiome.
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Authors: Beghini Francesco
Published: September 2024

Culture-independent analyses of microbial communities dramatically improved in the last decade, thanks to advances in methods for biological profiling via shotgun metagenomics and other molecular methods. This opens new opportunities for large-scale assembly efforts and the improvement of analysis tools with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated and improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes based on the largest set of reference sequences now available. MetaPhlAn 3 and HUMAnN 3 provides more accurate taxonomic and functional potential and activity profiles, respectively. These methods detected novel disease-microbiome links in CRC and IBD cohorts. Strain-level profiling of 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unravelled the phylogenetic and functional structure of the gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. Phylogenetic analysis with PhyloPhlAn 3 supports both genomic and metagenomic data, by assigning genomes from isolate sequencing or metagenomic assemblies to species-level genome bins defined on more than 230,000 publically available sequences. It also accurately reconstructs phylogenies at different resolutions (from strain-level to microbial tree-of-life) using maximally informative markers. The bioBakery 3 is open-source and includes documentation, training data, and cloud-deployable reproducible workflows to help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial communities. The ability to use metagenomic assemblies further help to study uncharacterized microbial species not represented by isolate genomes.

article: https://elifesciences.org/articles/65088
A three strain postbiotic mix improves the immune system function after oral intake for 28-days
Authors: Castellana Jordi Cuñé
Published: September 2024

Background: Dietary selenium complements are known to improve overall health and enhance different aspects of the immune response, participating in the function of the immune cells, cytokine secretion regulation of chronic inflammation and control of excessive immune responses. In this study, our objective was to evaluate whether a selenium-rich postbiotic composed of whole-cell Saccharomyces cerevisiae ABB S12, Kluyveromyces marxianus ABB S8 and Saccharomyces boulardii ABB S3 yeast strains, can act as provider of selenium to enhance the function of the human immune system after oral intake.
Methods and findings: A total of 15 volunteers were enrolled in a 28-day clinical study in which they complemented their normal diets with a daily dose of a novel selenium food supplement, “postbiotic immune”. Selenium levels in plasma were quantified by ELISA (Enzyme Linked Immuno Sorbent Assay), and the proliferation and activation of different subsets of lymphocytes isolated from PBMC’s (Peripheral Blood Mononuclear Cells) were assessed by flow cytometry using different cell markers. At the end of the study, we observed a higher proliferative capacity of total lymphocytes and specifically, of CD16+ lymphocytes (natural killer cells), upon stimulation with the CD3 and CD28 antibodies mimicking cell activation in vitro. Interestingly, we did not observe an increase in the activation of the lymphocyte subsets CD4+ (T helper cells) but CD16+, indicating that that there was a specific activation of natural killer cells.
Conclusions: Altogether, our results suggest that orally ingested ”Postbiotic immune” primes the human immune system to elicit a faster and more efficient immune response through the specific activation of natural killer cells.

Link to publication:
https://nutraceuticals.imedpub.com/a-three-strain-postbiotic-mix-improves-the-immune-system-function-after-oral-intake-for-28days.php?aid=52017
Human gut microbiome-dependent energy-extraction
Authors: Roager Henrik
Published: September 2024

More than 15 years ago, it was hypothesised that the gut microbiota could causally affect weight gain due to the gut microbiome’s capacity to extract energy from the diet. Yet, evidence linking microbiome-dependent energy harvest to particular human gut microbiome compositions have been lacking. In this recently published study, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and structure. We found opposite of what we expected that stool energy density was positively associated with intestinal transit time. Furthermore, individuals with a Bacteroides enterotype (B-type) had significantly lower energy left in faeces (per gram dried faeces) compared to individuals with a Ruminococcaecea enterotype (R-type). The B-type individuals had lower alpha-diversity and faster intestinal transit time, but also a significantly higher body weight compared to the R-type individuals. Furthermore, markers of proteolytic fermentation were increased in the R-type compared to the B-type. Together, this could suggest that human gut microbiome-dependent energy extraction is diversified according to intestinal transit time and gut microbiome ecosystem variations as reflected by enterotypes. While the causalities remain to be established, the observations are intriguing and could provide new dietary strategies in body weight management.

Link to OA paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01418-5
Time of Sample Collection Critical for Microbiome Replicability
Authors: Allaband Celeste
Published: September 2024

Although many aspects of microbiome studies have been standardized to improve experimental replicability, none account for how the daily diurnal fluctuations in the gut lumen cause dynamic changes in 16S amplicon sequencing. Here we show that sample collection time affects the conclusions drawn from microbiome studies and are larger than the effect size of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups are unique to each experiment. Sample collection times as short as only four hours apart lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. Without looking at other data, the impact on other fields is unknown but potentially significant.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.10.26.513817v1
Probing the Metatranscriptome of the House Mosquito Culex tritaeniorhynchus from the Philippines
Authors: Adiong Aldwin
Published: September 2024

Culex tritaeniorhynchus is a common household mosquito vector for arboviruses and filarial parasites. To circumvent the development of insecticide resistance, untargeted metatranscriptomics approaches in studying local Culex microbiomes can unveil potential paratransgenic vectors and critical host-microbiome interaction gene targets, serving as foundations for alternative vector biosurveillance and control methods. The metatranscriptomes generated from house mosquitoes collected from Barangays Bayog and Lalakay, Los Baños, Laguna, were pre-processed and host-filtered via fastp, bowtie2, and OpenContami. The clean dscDNA reads were then pooled per barangay and assembled using Trinity and metaSPAdes. Bacterial metatranscripts were retrieved for blastx annotation against the UniProt database, GO and KEGG analysis, and STRING protein-protein interaction network generation. Gram-negative bacterial genera Escherichia, Shigella, and Pseudomonas traceable to the local aquatic and human microflora chiefly contributed to the abundance of transcripts involved in antimicrobial resistance, secondary metabolite transport, aromatic amino acid biosynthesis, cell wall organization, genome regulation, two-component signaling, and iron cofactor metabolism.
Eight candidate prokaryotic genes were selected based on relative abundance and relevance to virulence, xenobiotic metabolism, and other adaptive functions. In both barangays and in select individual mosquitoes, all eight candidate genes were validated via RT-qPCR, exhibiting a wide range of Ct values and melt curve profiles. Genes involved in sustained survival against mosquito innate immune processes (enolases, peptidases, LPS remodelers) posit key players essential for the fitness of a potential paratransgenic vector. Individual variation in RT-qPCR detection results may hint at the relationship between the local and internal environments with respect to Culex microbiomes. As a pioneering metatranscriptomics study in the Philippines, we present potentially culturable paratransgenic vectors for Culex vector control, molecular mechanisms relevant to Culex-microbiome “interactomics”, and the role of environments in mediating the virulence of Culex parasites and symbionts. Recommendations include bacterial mRNA-enriched extraction protocols, in silico workflow integration with meta-omics datasets, and in vitro validation of culturable bacterial symbionts and their respective genes relevant for vector control.
Impact of gut decontamination on the intestinal microbiome composition and the risk of bloodstream infection (BSI) in pediatric allogeneic hematopoietic stem cell transplant (allo-HSCT) patients
Authors: Manara Serena
Published: September 2024

Research highlights
The effect of domestic water quality on the development of the infant gut microbiome
Authors: Parkin Kimberley
Published: September 2024

The infant gut microbiome begins development at birth, with major transition points occurring around the commencement of breastfeeding, the introduction of solid foods, and the cessation of breastfeeding. Until around three years of age, the development of the infant gut microbiome remains highly plastic and easily influenced by environmental factors. Developing a diverse and rich gut microbiome during this sensitive period is crucial to setting up a stable gut microbiome into adulthood, and to prevent gut dysbiosis. We have characterised the overall composition and functional profiles of the 6-month old gut microbiome using whole genome shotgun metagenomics sequencing and identified the key influencing environmental factors. Specifically, we discuss the effect of timing of solid food introduction, and feeding method on diversity. We also identified the differences in colonising species between breastfed and bottle-fed infants. We found the 6-month gut microbiome to be characterised by high rates of inter-individual variation. We also found infants fed exclusively formula milk had a higher overall diversity than infants fed a breastmilk diet and breastfed infants had a higher abundance of Bifidobacterium spp. We also did not identify any significantly different metabolic pathways between different environmental factors.
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans
Authors: Chia Minghao
Published: September 2024

Human blood is conventionally considered sterile but recent studies suggest the presence of a blood microbiome in healthy individuals. Here we characterized the DNA signatures of microbes in the blood of 9,770 healthy individuals using sequencing data from multiple cohorts. After filtering for contaminants, we identified 117 microbial species in blood, some of which had DNA signatures of microbial replication. They were primarily commensals associated with the gut (n = 40), mouth (n = 32) and genitourinary tract (n = 18), and were distinct from pathogens detected in hospital blood cultures. No species were detected in 84% of individuals, while the remainder only had a median of one species. Less than 5% of individuals shared the same species, no co-occurrence patterns between different species were observed and no associations between host phenotypes and microbes were found. Overall, these results do not support the hypothesis of a consistent core microbiome endogenous to human blood. Rather, our findings support the transient and sporadic translocation of commensal microbes from other body sites into the bloodstream.

Link to OA paper: https://www.nature.com/articles/s41564-023-01350-w
Understanding the Biodiversity of an Ecosystem Under Stress: Tales from Inflammatory Bowel Diseases
Authors: Eren A. Murat
Published: September 2024

A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished simply because disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. The purpose of this talk is to demonstrate how such microbes with 'high metabolic independence', characterized by the genomic presence of a set of key metabolic modules for the synthesis of essential nutrients dominate gut environments under stress. This paradigm depicts microbes as bystanders by default, rather than perpetrators or drivers of noncommunicable human diseases, and provides an ecological framework to explain the frequently observed reduction in microbial diversity associated with IBD and other noncommunicable human diseases and disorders.

Links to two OA papers and an OA perspective that may be appropriate material for further reading into this topic:
Watson, Fuessel, Veseli et al (2023): https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02924-x
Veseli et al (2023): https://elifesciences.org/reviewed-preprints/89862
Marcelino (2023): https://elifesciences.org/articles/92319
Exposure to environmental stressors decreases the resilience of river microbial communities towards invasion by foreign resistant bacteria
Authors: Bagra Kenyum
Published: September 2024

The release of wastewater treatment plant effluents into rivers exposes the river microbiome to a high load of antibiotic resistant bacteria (ARB) along with complex mixtures of abiotic pollutants acting as stressors.
To understand the proliferation of antimicrobial resistance (AMR) it is crucial to determine the factors that govern invasion of ARB into the river microbiome. Consequently, we here aim at elucidating how the resilience of the resident microbial communities against invasion by foreign ARB is affected by co-released stressors.
To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (E. coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.
In conclusion, we demonstrate that the intrinsic resilience of the river microbiome towards invasion by ARB is strongly linked with maintaining diversity and that co-exposure to stressors that disrupt community diversity and structure increases long-term invasion success.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.11.19.517188v1
Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host
Authors: Midha Ankur
Published: September 2024

Intestinal helminths are extremely prevalent among humans and animals. In particular, intestinal roundworms such as Ascaris suum affect more than 1 billion people around the globe and are a major issue in animal husbandry. These pathogens live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. Knowledge of the bacterial host microbiome at the site of infection is limited and data on the parasite microbiome is, to the best of our knowledge, non-existent. The intestinal microbiome of Ascaris suum was analyzed in contrast to the diversity and composition of the infected host gut. 16S sequencing of the parasite intestine and host intestinal compartments showed that the parasite gut has a significantly less diverse microbiome than its host and the host gut exhibits a reduced microbiome diversity at the site of parasite infection in the jejunum. While the host’s microbiome composition at the site of infection significantly determines the microbiome composition of its parasite, microbial signatures differentiate the nematodes from their hosts as the Ascaris intestine supports the growth of microbes that are otherwise under-represented in the host gut. Our data clearly indicate that a nematode infection reduces the microbiome diversity of the host gut and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut.

Link to OA paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01399-5
Pervasive selective sweeps across human gut microbiomes
Authors: Wolff Richard
Published: September 2024

The human gut microbiome is composed of a highly diverse consortia of species which are continually evolving within and across hosts. The ability to identify adaptations common to many host gut microbiomes would not only reveal shared selection pressures across hosts, but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, to date there has not been a systematic scan for adaptations that have spread across host microbiomes. Here, we develop a novel selection scan statistic, named the integrated linkage disequilibrium score (iLDS), that can detect the spread of adaptive haplotypes across host microbiomes via migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with the beneficial variant, a common feature of adaptive evolution. We find that iLDS is capable of detecting simulated and known cases of selection, and moreover is robust to potential confounders that can also elevate LD. Application of the statistic to ∼20 common commensal gut species from a large cohort of healthy, Western adults reveals pervasive spread of selected alleles across human microbiomes mediated by horizontal gene transfer. Among the candidate selective sweeps recovered by iLDS is an enrichment for genes involved in the metabolism of maltodextrin, a synthetic starch that has recently become a widespread component of Western diets. In summary, we demonstrate that selective sweeps across host microbiomes are a common feature of the evolution of the human gut microbiome.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2023.12.22.573162v1
Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study
Authors: Barnett David
Published: September 2024

The infant gut microbiota affects childhood health. This pioneer microbiota may be vulnerable to antibiotic exposures, but could be supported by prebiotic oligosaccharides found in breast milk and some infant formulas. We sought to characterize the effects of several exposures on the neonatal gut microbiota, including human milk oligosaccharides (HMOs), galacto-oligosaccharides (GOS), and infant/maternal antimicrobial exposures. We profiled the stool microbiota of 1023 one-month-old infants from the KOALA Birth Cohort using 16S rRNA gene amplicon sequencing. We quantified 15 HMOs in breast milk from the mothers of 220 infants, using high-performance liquid chromatography-mass spectrometry. Both breastfeeding and antibiotic exposure decreased gut microbial diversity, but each was associated with contrasting shifts in microbiota composition. Other factors associated with microbiota composition included C-section, homebirth, siblings, and exposure to animals. Neither infant exposure to oral antifungals nor maternal exposure to antibiotics during pregnancy were associated with infant microbiota composition. Four distinct groups of breast milk HMO compositions were evident, corresponding to maternal Secretor status and Lewis group combinations defined by the presence/absence of certain fucosylated HMOs. However, we found the strongest evidence for microbiota associations between two non-fucosylated HMOs: 6’-sialyllactose (6’-SL) and lacto-N-hexaose (LNH), which were associated with lower and higher relative abundances of Bifidobacterium, respectively. Among 111 exclusively formula-fed infants, the GOS-supplemented formula was associated with a lower relative abundance of Clostridium perfringens. In conclusion, the gut microbiota is sensitive to some prebiotic and antibiotic exposures during early infancy and understanding their effects could inform future strategies for safeguarding a health-promoting infant gut microbiota.

Link to OA paper: https://doi.org/10.1080/19490976.2022.2164152
A faecal microbiota signature with high specificity for pancreatic cancer
Authors: Kartal Ece
Published: September 2024

Following recent evidence suggesting a role for the microbiome in PDAC etiology and progression, we explored the fecal and salivary microbiota as potential diagnostic biomarkers. Design: We applied shotgun metagenomic and 16S rRNA amplicon sequencing to samples from a Spanish case-control study (N=136), including 57 cases, 50 controls, and 29 chronic pancreatitis patients in the discovery phase, and from a German case-control study (N=76), in the validation phase. Results: Fecal metagenomic classifiers performed much better than saliva-based ones and identified PDAC cases with an accuracy of up to 0.84 AUROC based on a set of 27 microbial species, with consistent accuracy across early and late disease stages. Performance further improved to up to 0.94 AUROC when we combined our microbiome-based predictions with serum levels of carbohydrate antigen (CA) 19-9, the only current non-invasive, FDA-approved, low specificity PDAC diagnostic biomarker. Furthermore, a microbiota-based classification model constrained to PDAC-enriched species was highly disease-specific when validated against 25 publicly available metagenomic study populations for various health conditions (N=5,792). Both microbiome-based models had a high prediction accuracy on an external German validation population (N=76). Several fecal PDAC marker species were detectable in pancreatic tumor and non-tumor tissue using 16S rRNA sequencing and fluorescence in situ hybridization. Conclusion: Taken together, our results indicate that non-invasive, robust and specific fecal microbiota-based screening for the early detection of PDAC is feasible.

Link to OA paper: https://gut.bmj.com/content/71/7/1359
The role of the gut microbiota in shaping responses to vaccination
Authors: Ryan Feargal
Published: September 2024

Global vaccination programs have been enormously successful, dramatically reducing the rates of vaccine-preventable diseases. However, for reasons that are poorly understood, these responses are highly variable between individuals. It is becoming increasingly apparent that the composition and function of the gut microbiota is a critical factor modulating immune responses to vaccination, and when the gut microbiota is disrupted, such as with antibiotic exposure, it may lead to suboptimal vaccine responses (e.g. lower antibody titres).
At the Lynn Systems Immunology group we use multi-omic technologies to study the relationship between the gut microbiota and vaccine responses in both humans and preclinical murine models. Here, I will report on findings from the Antibiotics and Immune Responses (AIR) study which followed 170 infants for the first 15 months of life to assess how early life antibiotic exposure shapes the composition of the gut microbiota, immune function and responses to scheduled infant vaccinations.
The Marie Project: The Vaginal Microbiome & Menstrual Health in Switzerland and Beyond
Authors: Ccenhua Monica R. Ticlla
Published: September 2024

Isala started in 2020 with more than 6000 women in Belgium willing to learn about their vaginal microbes and their relationship with their health. Today, Isala has inspired more than ten projects in other countries, united under the mission to improve women's health through investigation of the vaginal microbiome. This talk presents Marie, the Swiss sister project, and the first official collaboration between projects from the Isala sisterhood: Laura, Leke, Marie, and Isala. This collaboration interlinks fundamental biomedical research with social sciences methodologies to generate research evidence on the impact of menstrual products on the vaginal microbiome, complemented with women’s views, perceptions, and concerns about menstrual health management. Hand in hand with international policymakers, local organizations and the private sector, the four sisters want to bring knowledge of the impact of menstrual products on the vaginal microbiome to the current agenda on menstrual health.

Link: https://isala.be/en/the-isala-sisterhood-lets-write-history-together/
Fusobacterium nucleatum subspecies exhibit oral niche-specific biases
Authors: Krieger Madeline
Published: September 2024

Fusobacterium nucleatum, a ubiquitous member of the human oral and gut microbiomes, is strongly associated with the development of multiple human diseases including periodontitis, oral/extraoral abscesses, and several types of cancer. F. nucleatum is currently divided into four subspecies: F. nucleatum subspecies nucleatum (Fn. nucleatum), animalis (Fn. animalis), polymorphum (Fn. polymorphum), and vincentii/fusiforme (Fn. vincentii). Although these subspecies have been historically considered as functionally interchangeable, recent clinical studies of colorectal tumor-associated F. nucleatum have suggested this perception may be inaccurate. Consequently, we aimed to determine whether F. nucleatum subspecies prevalence in the oral cavity correlates with oral health status. Patient-matched specimens of dental plaque and odontogenic abscess were analyzed with both culture-independent and culture-dependent approaches using 58 and 44 paired samples, respectively. Pangenome, phylogenetic and functional enrichment analysis of Fusobacterium species and F. nucleatum subspecies were conducted using the Anvi’o workflow. Both culture-independent and -dependent analyses similarly revealed a highly biased distribution of F. nucleatum subspecies in the oral cavity, with most patients harboring multiple subspecies. In dental plaque, Fn. polymorphum is the dominant organism, whereas Fn. animalis is particularly prevalent within abscesses. Surprisingly, the most heavily studied subspecies, Fn. nucleatum, was only a minor constituent within the entire specimen collection. In agreement with the clinical data, phylogenetic and comparative genomic analyses identified substantial distinctions among F. nucleatum subspecies. The heterogeneous distribution of F. nucleatum subspecies within oral plaque and abscess specimens reveals niche-specific preferences, with Fn. animalis likely exhibiting the greatest pathogenic potential. Both the clinical and genomic data strongly suggest that each F. nucleatum subspecies likely comprises unique Fusobacterium species.
Assembly and dysbiosis of the seaweed microbiome
Authors: Egan Suhelen
Published: September 2024

Seaweeds are a ubiquitous group of photosynthetic organisms that play an essential role in many aquatic ecosystems. Seaweeds also host complex microbiomes. While symbiotic interactions with these microbiomes are essential for seaweeds, we now also know that microorganisms can be responsible for negative outcomes, such as disease of the host.
In this seminar I will firstly discuss how ecological principles such as the “lottery hypothesis” and “priority effects” determine how microbiomes assemble on seaweeds. Secondly, I will discuss how anthropogenic stressors can disturb the microbiome (i.e. cause dysbiosis) resulting in the proliferation of opportunistic pathogens leading to disease. Finally, I will describe recent studies that show mitigation of disease through the addition of beneficial microorganisms and their possible mode of action.
mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome
Authors: Cao Lei
Published: September 2024

Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that can sequence specific bacterial taxa of interest (pathogens, beneficial microbes, or low-abundance taxa), but not the vast background of other taxa in a microbiome sample. To address this need, we developed mEnrich-seq, a method that can enrich taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self vs. non-self genome differentiation provided by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes (REs), individually or in combination, to deplete host DNA and most background microbial DNA while enriching bacterial taxa of interest. This core idea is integrated with library preparation procedures in a way that only non-digested DNA libraries are sequenced. We performed in-depth evaluations of mEnrich-seq and demonstrated its use in several applications to enrich (up to 117-fold) genomic DNA of pathogenic or beneficial bacteria from human urine and fecal samples, including several species that are hard to culture or of low abundance. We also assessed the broad applicability of mEnrich-seq and found that 3130 (68.03%) of the 4601 strains with mapped methylomes to date can be targeted by at least one commercially available RE, representing 54.78% of the species examined in this analysis. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest directly from the microbiome.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.11.07.515285v1
Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome
Authors: Neugent Michael
Published: September 2024

Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary environment. However, changes in the urogenital microbiome underlying rUTI susceptibility are unknown. Here, we perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility. We identify candidate taxonomic biomarkers of rUTI susceptibility in postmenopausal women and an enrichment of lactobacilli in postmenopausal women taking estrogen hormone therapy. We find robust correlations between Bifidobacterium and Lactobacillus and urinary estrogens in women without urinary tract infection (UTI) history. Functional analyses reveal distinct metabolic and antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, we find that ARGs are enriched in the urogenital microbiomes of women with rUTI history independent of current UTI status. Our data suggest that rUTI and estrogen shape the urogenital microbiome in postmenopausal women.
Link to OA paper: https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(22)00302-0
BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men
Authors: Bowie Kate
Published: September 2024

Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS) such as urge urinary incontinence. However, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.
How heavy metals influence bacterial and fungal alpha-diversity in soil, sediment, and rhizosphere: A meta-analysis
Authors: Signorini Marco
Published: September 2024

Heavy metals (HMs) accumulation in soil affects plant growth and reduces the soil fauna diversity. Contrarily, the effect of HMs on microbial alpha-diversity remains an open question. Literature is contrasting, most likely because the microbial alpha-diversity variations strongly depend on heterogeneous and study-specific experimental conditions (e.g. soil type, soil chemical, physical and biological characteristics, type of metal considered, dose added etc.). Here, we report the first meta-analysis upon the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered the studies using the DNA metabarcoding of bacterial and fungal communities conducted between 2013 and 2021 to overcome some limitations of other techniques such as Denaturing Gradient Gel Electrophoresis (DGGE), or cultivation. This resulted in 66 independent experiments reported in 32 primary papers located over four continents. We found dose-dependent response to HMs for microbial alpha-diversity in bulk soil, rhizosphere soil and sediments. We further estimated that, on average, 17.5 mg kg-1 was the minimum inhibitory dose necessary to register a first significant loss (0.03 %) in microbial alpha-diversity compared to control conditions. However, such decline in alpha-diversity reached a maximum of 14.3 % for HMs additions peaking 5000 mg kg-1, irrespectively of the different experimental conditions. Our results suggest that extreme doses of Cu and Cd are necessary to have a consistent diversity loss, highlighting how the behaviour of microbial communities diverges from macro-organisms.
Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments
Authors: Bargheet Ahmed
Published: September 2024

Background: Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota’s core characteristics, gut resistome and mobilome, remains nascent. Methods: We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis. Findings: The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes. Interpretation: Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk.

Link to OA paper: https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00178-0/fulltext
HISTORICAL ESSAY BY ALEXANDER GUGNIN: BIBLIOGRAPHY AND PROBLEMS
Authors: LYSOVA N.
Published: September 2024

The article examines an essay by literary critic and translator A.A. Gugnin on literary relations between Germany and Russia. The scientist has been working on this topic for over 35 years. The essay became a conceptual reflection of the application of the author's historical and contextual method to the study of literature. Gugnin's thoroughly written Scientific work includes over 300 sources and is, in fact, an encyclopedic compendium of the stated topic. Russian Russian and German literary works, philologists, critics, artistic works of German and Russian literature from antiquity to the present day are mentioned and characterized by the author. He focuses on the typological parallels of the development of culture in different countries, presents the history of translations, the history of influences. All this gives him the op-portunity to state the general trends in the development of German-Russian literary relations.
INTERTEXTUALITY IN H. TURTLEDOVE’S «RULED BRITANNIA»
Authors: ALIAKSEYENKA Y.
Published: September 2024

The article deals with the specifics of intertextuality in H. Turtledove’s «Ruled Britannia», which belongs to alternative history genre, a kind of historiographical prose. W. Shakespeare’s and K. Marlowe’s works (tragedies, comedies, historical chronicles, a poem) are identified as precedent texts. The limited number of plays used by the author is due to the time of action (1597 – 1598), while some anachronisms are still allowed. It is revealed that the main form of reception for an American writer is the use of indirect quotations (allusions / reminiscences). It is established that the marking of precedent texts is carried out by mentioning the authorship., the names of plays and actors, interspersed with suggestive details of original plots. Other intertextual elements include proverbs, references to biblical and mythological sources (names, objects, details of the plot). The fictitional fragments of the «Boudicca» and «King Philip II», written by the hero-playwright, are based on the plays by W. Shakespeare, as well as his contemporaries (T. Hughes, J. Fletcher).
PORTRAIT OF AN ERA IN THE DISCOURSE OF BELARUSIAN MEDIA
Authors: RYZHKOVICH A.
Published: September 2024

The article substantiates the relevance of the study of keywords and combinations functioning in media discourse. Based on the texts of the online publication sb.by, attributive-substantive combinations with the word era are considered, acting as conceptual names for periods in the life of society that have signs of significance and duration. Ten semantic types of analytical names are identified. The basic characteristics are identified, on the basis of which long periods of time in the life of society are endowed with the property of “epoch-making”.
An Exegetical and Cultural Examination of “Shi er you ze xue, xue er you ze shi仕而优则学，学而优则仕”
Authors: Lian Yanting
Published: September 2024

“Shi er you ze xue, xue er you ze shi 仕而优则学，学而优则仕(An official versed in state affairs should amplify his knowledge; an intellectual well equipped with knowledge should serve the state.)” was put forward by Confucian scholars during the Spring and Autumn Period in the light of the social reality that many people had not yet learned to serve, but its connotation was often misinterpreted by later generations as “the theory of studying to become a government official”. Examined from an exegetical and cultural point of view, it can be seen that “xue学” refers to the study of moral and etiquette norms and knowledge of literature, and “you优” means “abundance, spare capacity”. “shi仕” refers to being an official; ‘Shi er you ze xue仕而优则学’ is a compromise way adopted by Confucianism to solve the contradiction between ideals and reality; ‘xue er you学而优’ is the prerequisite for ‘shi仕’; and ‘shi仕’ is a bridge for Confucianism to realize the ideal of helping the world.
Faktor-faktor yang memengaruhi return saham dengan kebijakan dividen sebagai variabel moderasi pada perusahaan sektor energi yang terdaftar di BEI tahun 2018-2022
Authors: Sari Ira Puspita , Astuti Diana Dwi , Ilmi Mainatul
Published: September 2024

This study aims to analyze the effect of profitability, leverage, and company size on stock returns and the role of dividend policy as a moderating variable in energy sector companies listed on the Indonesia Stock Exchange for 2018-2022. The sampling technique in this study used a purposive sampling technique, which resulted in 15 companies as research samples from a total population of 84 companies. The data analysis method used is the moderation regression analysis. The results showed that profitability has a significant effect on stock returns. Leverage has no significant effect on stock returns. Company size has no significant effect on stock returns. Dividend policy can act as a moderating variable for the effect of profitability on stock returns. Dividend policy cannot act as a moderating variable for the effect of leverage on stock returns. Dividend policy can act as a moderating variable for the effect of company size on stock returns.