bluuebunny/crossref_metadata_2025_split huggingface dataset:
DA PROFISSIONALIZAÇÃO AO DESENVOLVIMENTO PROFISSIONAL DOCENTE: EM DESTAQUE AS POLÍTICAS EDUCACIONAIS BRASILEIRAS
Authors: Ximenes Priscilla de Andrade Silva , Melo Geovana Ferreira , Magalhães Solange Martins Oliveira 
Published: September 2024

O presente artigo é oriundo de uma pesquisa bibliográfica que objetivou compreender as diferentes acepções e uso do termo Desenvolvimento Profissional Docente no contexto das políticas educacionais, buscando desvelar as concepções que sustentam as políticas educacionais e como elas se atrelam com a formação, carreira e trabalho docente. Para tanto, consideramos uma abordagem historicizante e crítica dos relatórios oficiais e políticas de formação docente provenientes das investidas de agências e organismos internacionais, a partir das reformas educacionais da década de 1990. Constata-se que apesar da relação que é estabelecida entre o conceito de DPD e de profissionalização docente, o seu uso no campo das políticas educacionais brasileiras tende a desconsiderar o movimento sócio-histórico de (des)valorização profissional docente.
Does genome contamination compromise the GTDB taxonomy?
Authors: Hugenholtz Phil 
Published: September 2024

Recently, the Bork group published a tool called GUNC (the Genome UNClutter) that detects chimerism and contamination in prokaryotic genomes. Disturbingly, they estimated that 3.2% (1009) of all species in release 95 of the Genome Taxonomy Database (GTDB) consist entirely of contaminated genomes, which could inflate estimates of phylogenetic diversity and taxonomic novelty. We applied GUNC to the latest release of GTDB and found the situation is even worse, with 6.0% (3,958) of all species in release 207 estimated to be comprised entirely of contaminated genomes.To address the question of whether this contamination compromises the GTDB taxonomy by inflating phylogenetic diversity, we split putative chimeric genomes into halves according to their GUNC contamination scores. We then inferred phylogenetic trees from the genome halves as per the standard GTDB workflow, i.e. based on a concatenated alignment of up to 120 single copy marker genes, to determine any changes in genus to phylum classifications between pairs of genome halves. We also subjected the genome halves to average nucleotide identity (ANI)-based analysis, which is how species are assigned in GTDB. These analyses allowed us to quantify taxonomic inflation caused by genomic contamination, and the extent to which the GTDB taxonomy has been compromised. Tune in to find out the results!
Advances in cpn60 barcoding for microbial species identification
Authors: Hill Janet 
Published: September 2024

The “universal target” region of the gene encoding the 60 kDa chaperonin protein (cpn60, also known as groEL or hsp60) is a proven sequence barcode for bacteria and a useful target for marker gene amplicon-based studies of complex microbial communities. Application of cpn60 barcode sequencing is facilitated by 'universal' amplification primers and cpnDB, a manually curated reference database of cpn60 sequences. Recent developments to the cpn60 platform include demonstration that 150 bp from the 5' end of the barcode is sufficient for species level resolution of bacteria. These short sequences can be identified using established sequence classifiers (QIIME2 feature classifier and RDP classifier), making it simple to integrate cpn60 amplicon sequence identification into existing microbiome analysis pipelines, as recently demonstrated for human skin, vaginal, salivary and stool microbiomes. The purpose of this presentation is to provide a brief overview of cpn60 barcoding resources and applications, and to highlight recent research advances.Link to OA paper: https://www.nature.com/articles/s43705-023-00283-z
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
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
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
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
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 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