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1. Genital tract microbiome dynamics are associated with time of Chlamydia infection in mice

   https://doi.org/10.1038/s41598-023-36130-3  

   Zhao, Lihong; Lundy, Stephanie R.; Eko, Francis O.; Igietseme, Joeseph U.; Omosun, Yusuf O. (December 2023, Scientific Reports)

   Abstract We have previously shown that the time ofChlamydiainfection was crucial in determining the chlamydial infectivity and pathogenesis. This study aims to determine whether the time ofChlamydiainfection affects the genital tract microbiome. This study analyzed mice vaginal, uterine, and ovary/oviduct microbiome with and withoutChlamydiainfection. The mice were infected withChlamydiaat either 10:00 am (ZT3) or 10:00 pm (ZT15). The results showed that mice infected at ZT3 had higherChlamydiainfectivity than those infected at ZT15. There was more variation in the compositional complexity of the vaginal microbiome (alpha diversity) of mice infected at ZT3 than those mice infected at ZT15 throughout the infection within each treatment group, with both Shannon and Simpson diversity index values decreased over time. The analysis of samples collected four weeks post-infection showed that there were significant taxonomical differences (beta diversity) between different parts of the genital tract—vagina, uterus, and ovary/oviduct—and this difference was associated with the time of infection.FirmicutesandProteobacteriawere the most abundant phyla within the microbiome in all three genital tract regions for all the samples collected during this experiment. Additionally,Firmicuteswas the dominant phylum in the uterine microbiome of ZT3Chlamydiainfected mice. The results show that the time of infection is associated with the microbial dynamics in the genital tract. And this association is more robust in the upper genital tract than in the vagina. This result implies that more emphasis should be placed on understanding the changes in the microbial dynamics of the upper genital tract over the course of infection. 

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2. Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer

   https://doi.org/s12885-021-08530-z  

   Justin, Chau; Meeta, Yadav; Ben, Liu; Muhammad, Furqan; Qun, Dai; Shailesh, Shahi; Arnav, Gupta; Keri, Nace Mercer; Evan, Eastman; Taher, Abu Hejleh; et al (October 2021, BMC cancer)

   Background Though the gut microbiome has been associated with efficacy of immunotherapy (ICI) in certain cancers, similar findings have not been identified for microbiomes from other body sites and their correlation to treatment response and immune related adverse events (irAEs) in lung cancer (LC) patients receiving ICIs. Methods We designed a prospective cohort study conducted from 2018 to 2020 at a single-center academic institution to assess for correlations between the microbiome in various body sites with treatment response and development of irAEs in LC patients treated with ICIs. Patients must have had measurable disease, ECOG 0–2, and good organ function to be included. Data was collected for analysis from January 2019 to October 2020. Patients with histopathologically confirmed, advanced/metastatic LC planned to undergo immunotherapy-based treatment were enrolled between September 2018 and June 2019. Nasal, buccal and gut microbiome samples were obtained prior to initiation of immunotherapy +/− chemotherapy, at development of adverse events (irAEs), and at improvement of irAEs to grade 1 or less. Results Thirty-seven patients were enrolled, and 34 patients were evaluable for this report. 32 healthy controls (HC) from the same geographic region were included to compare baseline gut microbiota. Compared to HC, LC gut microbiota exhibited significantly lower α-diversity. The gut microbiome of patients who did not suffer irAEs were found to have relative enrichment of Bifidobacterium (p = 0.001) and Desulfovibrio (p = 0.0002). Responders to combined chemoimmunotherapy exhibited increased Clostridiales (p = 0.018) but reduced Rikenellaceae (p = 0.016). In responders to chemoimmunotherapy we also observed enrichment of Finegoldia in nasal microbiome, and increased Megasphaera but reduced Actinobacillus in buccal samples. Longitudinal samples exhibited a trend of α-diversity and certain microbial changes during the development and resolution of irAEs. Conclusions This pilot study identifies significant differences in the gut microbiome between HC and LC patients, and their correlation to treatment response and irAEs in LC. In addition, it suggests potential predictive utility in nasal and buccal microbiomes, warranting further validation with a larger cohort and mechanistic dissection using preclinical models. 

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3. Computational Methods to Study Human Transcript Variants in COVID-19 Infected Lung Cancer Cells

   https://doi.org/10.3390/ijms22189684  

   Sun, Jiao; Fahmi, Naima Ahmed; Nassereddeen, Heba; Cheng, Sze; Martinez, Irene; Fan, Deliang; Yong, Jeongsik; Zhang, Wei (September 2021, International Journal of Molecular Sciences)

   null (Ed.)

   Microbes and viruses are known to alter host transcriptomes by means of infection. In light of recent challenges posed by the COVID-19 pandemic, a deeper understanding of the disease at the transcriptome level is needed. However, research about transcriptome reprogramming by post-transcriptional regulation is very limited. In this study, computational methods developed by our lab were applied to RNA-seq data to detect transcript variants (i.e., alternative splicing (AS) and alternative polyadenylation (APA) events). The RNA-seq data were obtained from a publicly available source, and they consist of mock-treated and SARS-CoV-2 infected (COVID-19) lung alveolar (A549) cells. Data analysis results show that more AS events are found in SARS-CoV-2 infected cells than in mock-treated cells, whereas fewer APA events are detected in SARS-CoV-2 infected cells. A combination of conventional differential gene expression analysis and transcript variants analysis revealed that most of the genes with transcript variants are not differentially expressed. This indicates that no strong correlation exists between differential gene expression and the AS/APA events in the mock-treated or SARS-CoV-2 infected samples. These genes with transcript variants can be applied as another layer of molecular signatures for COVID-19 studies. In addition, the transcript variants are enriched in important biological pathways that were not detected in the studies that only focused on differential gene expression analysis. Therefore, the pathways may lead to new molecular mechanisms of SARS-CoV-2 pathogenesis. 

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4. Transcriptional activity differentiates families of Marine Group II Euryarchaeota in the coastal ocean

   https://doi.org/10.1038/s43705-021-00002-6  

   Damashek, Julian; Okotie-Oyekan, Aimee Oyinlade; Gifford, Scott Michael; Vorobev, Alexey; Moran, Mary Ann; Hollibaugh, James Timothy (December 2021, ISME Communications)

   null (Ed.)

   Abstract Marine Group II Euryarchaeota ( Candidatus Poseidoniales), abundant but yet-uncultivated members of marine microbial communities, are thought to be (photo)heterotrophs that metabolize dissolved organic matter (DOM), such as lipids and peptides. However, little is known about their transcriptional activity. We mapped reads from a metatranscriptomic time series collected at Sapelo Island (GA, USA) to metagenome-assembled genomes to determine the diversity of transcriptionally active Ca . Poseidoniales. Summer metatranscriptomes had the highest abundance of Ca . Poseidoniales transcripts, mostly from the O1 and O3 genera within Ca . Thalassarchaeaceae (MGIIb). In contrast, transcripts from fall and winter samples were predominantly from Ca . Poseidoniaceae (MGIIa). Genes encoding proteorhodopsin, membrane-bound pyrophosphatase, peptidase/proteases, and part of the ß-oxidation pathway were highly transcribed across abundant genera. Highly transcribed genes specific to Ca . Thalassarchaeaceae included xanthine/uracil permease and receptors for amino acid transporters. Enrichment of Ca . Thalassarchaeaceae transcript reads related to protein/peptide, nucleic acid, and amino acid transport and metabolism, as well as transcript depletion during dark incubations, provided further evidence of heterotrophic metabolism. Quantitative PCR analysis of South Atlantic Bight samples indicated consistently abundant Ca . Poseidoniales in nearshore and inshore waters. Together, our data suggest that Ca . Thalassarchaeaceae are important photoheterotrophs potentially linking DOM and nitrogen cycling in coastal waters. 

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5. Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples

   https://doi.org/10.1093/jmammal/gyae153  

   Peralta_Martínez, Karen Y; Goyco-Blas, José; Reilly, Sarah M; Ahn, Young; Hedayati, Stefanie; Kohl, Kevin D (January 2025, Journal of Mammalogy)

   Alston, Jesse (Ed.)

   The field of microbial ecology is increasingly recognizing the need for methods to isolate and culture gut microbes to better understand how these microorganisms impact animal physiology, especially in mammalian hosts. Currently, there is a lack of clear methods to store microbial samples for cultivability, especially when samples are collected from the field, transported to the laboratory, and preserved under long-term storage for weeks to months compared to mere days in the biomedical field. Here, the cecal contents of groundhogs (Marmota monax) were processed and stored with or without various preservation solutions at −80 °C for at least 2 months. All microbial samples were then grown in distinct nutrient media in liquid and plate conditions and were incubated under anaerobic and aerobic environments. Treatment comparisons revealed that the samples stored in preservation solutions containing 1 or more cryoprotectants provided the greatest and most consistent bacterial densities. To test the long-term storage efficacy of the preservation solutions, we inventoried taxonomic identities and abundances of these cultures using 16S rRNA amplicon sequencing. Our findings highlight that: (1) preserved samples containing cryoprotectants exhibited the highest microbial richness and diversity and resembled the original cecal samples the most when grown under anaerobic conditions; and (2) the effect of individual animal identity was detectable in the membership of cultured communities, irrespective of preservation solutions. Our study is the first to demonstrate the importance of preservation solutions containing multiple cryoprotectants for long-term storage and further microbial culturing and novel isolation. Understanding and improving storage methods that preserve microbial physiology and conserve their compositional diversity is essential for field-collected samples useful in mammalian microbiome and culturomics studies, promoting a better comprehension of the identity and function of wild host-associated microbiomes. 

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