bluuebunny/crossref_metadata_2025_split huggingface dataset:
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 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/
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
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
Encuesta a las empresas españolas sobre la evolución de su actividad: tercer trimestre de 2024
Authors: Fernández Cerezo Alejandro , Izquierdo Mario 
Published: September 2024

Motivación
La Encuesta del Banco de España sobre la Actividad Empresarial (EBAE) permite extraer, en tiempo real, información muy valiosa acerca de la facturación, el empleo y los precios pagados y cobrados por una muestra amplia de empresas españolas, lo que proporciona una contribución muy relevante al diagnóstico de la situación coyuntural de la economía.
Ideas principales
•Las empresas perciben un descenso de la facturación en el tercer trimestre de 2024, aunque de menor magnitud que la caída registrada en el mismo trimestre de los dos años anteriores.
•Las presiones inflacionistas siguen disminuyendo en el tercer trimestre, tanto en términos del coste de los inputs como de los precios de venta y de los costes laborales.
•La incidencia negativa de la incertidumbre sobre la política económica, los problemas de disponibilidad de mano de obra y del aumento de los costes energéticos sigue siendo elevada, pero desciende el porcentaje de compañías afectadas por factores relacionados con el acceso a la financiación y al aumento de los gastos financieros.
Las variables sociodemográficas y su relación con el síndrome Burnout (SBO) en administrativos de la Universidad Francisco de Paula Santander Ocaña
Authors: Torrado Peñaranda Ana Karina , Peñaranda Peñaranda Marta Milena , Suárez Castrillón Sir-Alexci 
Published: September 2024

Las pretensiones de la investigación van encaminadas a determinar la relación entre las variables sociodemográficas y el síndrome Burnout en el personal administrativo de la Universidad Francisco de Paula Santander Ocaña, la cual precisó de una metodología de investigación con enfoque cuantitativo de tipo transversal descriptivo, realizado a una población finita de administrativos contemplando datos sociodemográficos como sexo, condición laboral, edad y estado civil, seguido de la aplicación de la escala Maslach Burnout Inventory constituido por 16 ítems que abordan las dimensiones de agotamiento, cinismo y eficacia. Los hallazgos revelaron que una pequeña población de hombres y mujeres sin muchas diferencias marcadas comienza a padecer el síndrome burnout, así mismo el tipo de contratación nombrado y contratado alertan igualmente la presencia del síndrome. En relación con la edad se apreciaron ligeras diferencias al identificar que sin importar la edad el personal se encuentra con toda la energía para seguir realizando su trabajo, mientras que en la dimensión cinismo se presentan niveles medios y altos en la pérdida de motivación hacia el trabajo, haciéndose más visible esta pérdida cuando han superado la edad de 45 años y su eficacia este grupo solo alcanza niveles bajos y medios. Para la variable sociodemográfica de estado civil el grupo con mayor riesgo ante el síndrome burnout es el estado civil casados. La presencia de este riesgo demanda el interés de la institución.
The Effectiveness of Functional Training of Female Students with Low Physical Fitness Test Score
Authors: Guo Wei 
Published: September 2024

In view of the development of society and lifestyle, contemporary college students are faced with many problems in physical health, especially the decline of physical fitness level of college students, which urgently need effective intervention. This study used a quasi-experimental approach to explore functional training as a way to improve the physical fitness of female college students who scored low or failed in the physical fitness test. The aim is to explore the effectiveness of functional training for female students with low fitness test scores. The results showed that functional training significantly improved the physical level of female students, especially on 50 m, curling, 1-minute sit-up and stand, long jump. In addition, at 800 meters, the functional training effect is inferior to the traditional training effect. This shows that functional training has obvious effect on the speed, strength and flexibility of female universities with low scores, but not on endurance programs.The results emphasize the functional training as a low physical students overall health level is an effective method.
Impact of Teaching Styles of Tennis Coaches on Students’ Performance
Authors: Chen Dongdong 
Published: September 2024

To understand the teaching styles employed in most of the Chinese universities in Henan Province, this research will assess the teaching styles of coaches from three (3) selected universities in the province based on their students’ perspectives. It will further evaluate the performance of the students so as to connect or find the link between the teaching styles and the students’ performances in tennis classes. The researcher employed a descriptive-comparative-correlational approach. The results indicate that teachers play a crucial role in imparting information, knowledge, and skills, ensuring holistic growth and readiness for complex concepts. The teaching styles of the tennis coaches at the universities promote confidence, trust, and continuous interest in the field, emphasizing clear explanations, structured presentations, and direct instructional methods. Tennis coaches in participating universities in Henan Province provide students with a learning structure, a positive teacher image, and effective teaching strategies. These strategies include creating learning goals, expectations, and rules of contact and emphasizing precise standards and practical approaches. Moreover, the data showed that effectively using limited resources and integrating physical activity into their teaching plays a great role in achieving excellent student performance. The researcher recommends developing an intervention that will focus on increasing the confidence of students to utilize their learning about tennis in a professional setting. It is also advisable to create a study that focuses on teachers’ perceptions of the availability of materials and how it improves their teaching styles and performance as educators, affecting their confidence and motivation.