@article {pmid38749891,
year = {2024},
author = {Marsh, R and Santos, CD and Yule, A and Dellschaft, NS and Hoad, CL and Ng, C and Major, G and Smyth, AR and Rivett, D and van der Gast, C},
title = {Impact of extended Elexacaftor/Tezacaftor/Ivacaftor therapy on the gut microbiome in cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2024.05.002},
pmid = {38749891},
issn = {1873-5010},
abstract = {BACKGROUND: There is a paucity of knowledge on the longer-term effects of CF transmembrane conductance regulator (CFTR) modulator therapies upon the gut microbiome and associated outcomes. In a pilot study, we investigated longitudinal Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy on the gut microbiota, metabolomic functioning, and clinical outcomes in people with CF (pwCF).

STUDY DESIGN: Faecal samples from 20 pwCF were acquired before and then following 3, 6, and 17+ months of ETI therapy. Samples were subjected to microbiota sequencing and targeted metabolomics to profile and quantify short-chain fatty acid composition. Ten healthy matched controls were included for comparison. Clinical data, including markers of intestinal function were integrated to investigate relationships.

RESULTS: Extended ETI therapy increased core microbiota diversity and composition, which translated to gradual shifts in whole microbiota composition towards that observed in healthy controls. Despite becoming more similar over time, CF microbiota and functional metabolite compositions remained significantly different to healthy controls. Antibiotic treatment for pulmonary infection significantly explained a relatively large degree of variation within the whole microbiota and rarer satellite taxa. Clinical outcomes were not significantly different following ETI.

CONCLUSIONS: Whilst differences persisted, a positive trajectory towards the microbiota observed in healthy controls was found. We posit that progression was predominately impeded by pulmonary antibiotics administration. We recommend future studies use integrated omics approaches within a combination of long-term longitudinal patient studies and model experimental systems. This will deepen our understanding of the impacts of CFTR modulator therapy and respiratory antibiotic interventions upon the gut microbiome and gastrointestinal pathophysiology in CF.},
}

@article {pmid38749279,
year = {2024},
author = {Dulamea, AO and Lupescu, IC},
title = {Cerebral cavernous malformations - An overview on genetics, clinical aspects and therapeutic strategies.},
journal = {Journal of the neurological sciences},
volume = {461},
number = {},
pages = {123044},
doi = {10.1016/j.jns.2024.123044},
pmid = {38749279},
issn = {1878-5883},
abstract = {Cerebral cavernous malformations (CCMs) are abnormally packed blood vessels lined with endothelial cells, that do not exhibit intervening tight junctions, lack muscular and elastic layers and are usually surrounded by hemosiderin and gliosis. CCMs may be sporadic or familial autosomal dominant (FCCMs) caused by loss of function mutations in CCM1 (KRIT1), CCM2 (MGC4607), and CCM3 (PDCD10) genes. In the FCCMs, patients have multiple CCMs, different family members are affected, and developmental venous anomalies are absent. CCMs may be asymptomatic or may manifest with focal neurological deficits with or without associated hemorrhage andseizures. Recent studies identify a digenic "triple-hit" mechanism involving the aquisition of three distinct genetic mutations that culminate in phosphatidylinositol-3-kinase (PIK3CA) gain of function, as the basis for rapidly growing and clinically symptomatic CCMs. The pathophysiology of CCMs involves signaling aberrations in the neurovascular unit, including proliferative dysangiogenesis, blood-brain barrier hyperpermeability, inflammation and immune mediated processes, anticoagulant vascular domain, and gut microbiome-driven mechanisms. Clinical trials are investigating potential therapies, magnetic resonance imaging and plasma biomarkers for hemorrhage and CCMs-related epilepsy, as well as different techniques of neuronavigation and neurosonology to guide surgery in order to minimize post-operatory morbidity and mortality. This review addresses the recent data about the natural history, genetics, neuroimaging and therapeutic approaches for CCMs.},
}

@article {pmid38749249,
year = {2024},
author = {Wang, Y and Zhang, F and Zhang, G and Wang, H and Zhu, S and Zhang, H and He, T and Guo, T},
title = {Trace metals coupled with plasticisers in microplastics strengthen the denitrification function of the soil microbiome in the Qinghai Tibetan Plateau.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134593},
doi = {10.1016/j.jhazmat.2024.134593},
pmid = {38749249},
issn = {1873-3336},
abstract = {Due to the lack of research on the co-effects of microplastics and trace metals in the environment on nitrogen cycling-related functional microorganisms, the occurrence of microplastics and one of their plasticisers, phthalate esters, as well as trace metals, were determined in soils and river sediments in the Qinghai-Tibet Plateau. Relationship between microplastics and phthalate esters in the area was determined; the co-effects of these potentially toxic materials, and key factors and pathways affecting nitrogen functions were further explored. Significant correlations between fibre- and film-shaped microplastics and phthalate esters were detected in the soils from the plateau. Copper, lead, cadmium and di-n-octyl phthalate detected significantly affected nitrogen cycling-related functional microorganisms. The co-existence of di-n-octyl phthalate and copper in soils synergistically stimulated the expression of denitrification microorganisms nirS gene and "nitrate_reduction". Additionally, di-n-octyl phthalate and dimethyl phthalate more significantly affected the variation of nitrogen cycling-related functional genes than the number of microplastics. In a dimethyl phthalate- and cadmium-polluted area, nitrogen cycling-related functional genes, especially nirK gene, were more sensitive and stressed. Overall, phthalate esters originated from microplastics play a key role in nitrogen cycling-related functions than microplastics themselves, moreover, the synergy between di-n-octyl phthalate and copper strengthen the expression of denitrification functions.},
}

@article {pmid38749246,
year = {2024},
author = {Yang, S and Han, X and Li, J and Luan, F and Zhang, S and Han, D and Yang, M and Chen, Q and Qi, Z},
title = {Oceanobacillus picturae alleviates cadmium stress and promotes growth in soybean seedlings.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134568},
doi = {10.1016/j.jhazmat.2024.134568},
pmid = {38749246},
issn = {1873-3336},
abstract = {Cadmium (Cd) is a heavy metal that significantly impacts human health and the environment. Microorganisms play a crucial role in reducing heavy metal stress in plants; however, the mechanisms by which microorganisms enhance plant tolerance to Cd stress and the interplay between plants and microorganisms under such stress remain unclear. In this study, Oceanobacillus picturae (O. picturae) was isolated for interaction with soybean seedlings under Cd stress. Results indicated that Cd treatment alone markedly inhibited soybean seedling growth. Conversely, inoculation with O. picturae significantly improved growth indices such as plant height, root length, and fresh weight, while also promoting recovery in soil physiological indicators and pH. Metabolomic and transcriptomic analyses identified 157 genes related to aspartic acid, cysteine, and flavonoid biosynthesis pathways. Sixty-three microbial species were significantly associated with metabolites in these pathways, including pathogenic, adversity-resistant, and bioconductive bacteria. This research experimentally demonstrates, for the first time, the growth-promoting effect of the O. picturae strain on soybean seedlings under non-stress conditions. It also highlights its role in enhancing root growth and reducing Cd accumulation in the roots under Cd stress. Additionally, through the utilization of untargeted metabolomics, metagenomics, and transcriptomics for a multi-omics analysis, we investigated the impact of O. picturae on the soil microbiome and its correlation with differential gene expression in plants. This innovative approach unveils the molecular mechanisms underlying O. picturae's promotion of root growth and adaptation to Cd stress.},
}

@article {pmid38748886,
year = {2024},
author = {Adhikary, K and Sarkar, R and Maity, S and Banerjee, I and Chatterjee, P and Bhattacharya, K and Ahuja, D and Sinha, NK and Maiti, R},
title = {The underlying causes, treatment options of gut microbiota and food habits in type 2 diabetes mellitus: a narrative review.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {},
number = {},
pages = {},
pmid = {38748886},
issn = {2191-0286},
abstract = {Type 2 diabetes mellitus is a long-lasting endocrine disorder characterized by persistent hyperglycaemia, which is often triggered by an entire or relative inadequacy of insulin production or insulin resistance. As a result of resistance to insulin (IR) and an overall lack of insulin in the body, type 2 diabetes mellitus (T2DM) is a metabolic illness that is characterized by hyperglycaemia. Notably, the occurrence of vascular complications of diabetes and the advancement of IR in T2DM are accompanied by dysbiosis of the gut microbiota. Due to the difficulties in managing the disease and the dangers of multiple accompanying complications, diabetes is a chronic, progressive immune-mediated condition that plays a significant clinical and health burden on patients. The frequency and incidence of diabetes among young people have been rising worldwide. The relationship between the gut microbiota composition and the physio-pathological characteristics of T2DM proposes a novel way to monitor the condition and enhance the effectiveness of therapies. Our knowledge of the microbiota of the gut and how it affects health and illness has changed over the last 20 years. Species of the genus Eubacterium, which make up a significant portion of the core animal gut microbiome, are some of the recently discovered 'generation' of possibly helpful bacteria. In this article, we have focused on pathogenesis and therapeutic approaches towards T2DM, with a special reference to gut bacteria from ancient times to the present day.},
}

@article {pmid38748788,
year = {2024},
author = {Zhao, Z and Amano, C and Reinthaler, T and Orellana, MV and Herndl, GJ},
title = {Substrate uptake patterns shape niche separation in marine prokaryotic microbiome.},
journal = {Science advances},
volume = {10},
number = {20},
pages = {eadn5143},
pmid = {38748788},
issn = {2375-2548},
mesh = {*Microbiota ; Seawater/microbiology ; Prokaryotic Cells/metabolism ; ATP-Binding Cassette Transporters/metabolism ; Substrate Specificity ; Phylogeny ; Bacteria/metabolism/classification ; Aquatic Organisms/metabolism ; Membrane Transport Proteins/metabolism ; Carbon/metabolism ; },
abstract = {Marine heterotrophic prokaryotes primarily take up ambient substrates using transporters. The patterns of transporters targeting particular substrates shape the ecological role of heterotrophic prokaryotes in marine organic matter cycles. Here, we report a size-fractionated pattern in the expression of prokaryotic transporters throughout the oceanic water column due to taxonomic variations, revealed by a multi-"omics" approach targeting ATP-binding cassette (ABC) transporters and TonB-dependent transporters (TBDTs). Substrate specificity analyses showed that marine SAR11, Rhodobacterales, and Oceanospirillales use ABC transporters to take up organic nitrogenous compounds in the free-living fraction, while Alteromonadales, Bacteroidetes, and Sphingomonadales use TBDTs for carbon-rich organic matter and metal chelates on particles. The expression of transporter proteins also supports distinct lifestyles of deep-sea prokaryotes. Our results suggest that transporter divergency in organic matter assimilation reflects a pronounced niche separation in the prokaryote-mediated organic matter cycles.},
}

*Microbiota
Seawater/microbiology
Prokaryotic Cells/metabolism
ATP-Binding Cassette Transporters/metabolism
Substrate Specificity
Phylogeny
Bacteria/metabolism/classification
Aquatic Organisms/metabolism
Membrane Transport Proteins/metabolism
Carbon/metabolism

@article {pmid38748495,
year = {2024},
author = {Zhao, W and Ren, A and Shan, S and Li, Z and Su, R and Yang, R and Zhai, F and Wu, L and Tang, Z and Yang, J and Yue, L},
title = {Inhibitory Effects of Soluble Dietary Fiber from Foxtail Millet on Colorectal Cancer by the Restoration of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c00867},
pmid = {38748495},
issn = {1520-5118},
abstract = {Colorectal cancer (CRC) is a common malignant tumor that occurs in the colon. Gut microbiota is a complex ecosystem that plays an important role in the pathogenesis of CRC. Our previous studies showed that the soluble dietary fiber of foxtail millet (FMB-SDF) exhibited significant antitumor activity in vitro. The present study evaluated the anticancer potential of FMB-SDF in the azoxymethane (AOM)- and dextran sodium sulfate (DSS)-induced mouse CRC models. The results showed that FMB-SDF could significantly alleviate colon cancer symptoms in mice. Further, we found that FMB-SDF consumption significantly altered gut microbiota diversity and the overall structure and regulated the abundance of some microorganisms in CRC mice. Meanwhile, KEGG pathway enrichment showed that FMB-SDF can also alleviate the occurrence of colon cancer in mice by regulating certain cancer-related signaling pathways. In conclusion, our findings may provide a novel approach for the prevention and biotherapy of CRC.},
}

@article {pmid38748355,
year = {2024},
author = {Wang, J and Li, Y and Mu, Y and Huang, K and Li, D and Lan, C and Cui, Y and Wang, J},
title = {Missing microbes in infants and children in the COVID-19 pandemic: a study of 1,126 participants in Beijing, China.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {38748355},
issn = {1869-1889},
abstract = {The COVID-19 pandemic has caused many fatalities worldwide and continues to affect the health of the recovered patients in the form of long-COVID. In this study, we compared the gut microbiome of uninfected infants and children before the pandemic began (BEFORE cohort, n=906) to that of after the pandemic (AFTER cohort, n=220) to examine the potential impact of social distancing and life habit changes on infant/children gut microbiome. Based on 16S rRNA sequencing, we found a significant change in microbiome composition after the pandemic, with Bacteroides enterotype increasing to 35.45% from 30.46% before the pandemic. qPCR quantification indicated that the bacterial loads of seven keystone taxa decreased by 91.69%-19.58%. Quantitative microbiome profiling, used to enhance the resolution in detecting microbiome differences, revealed a greater explained variance of pandemic on microbiome compared to gender, as well as a significant decrease in bacterial loads in 15 of the 20 major genera. The random forest age-predictor indicated the gut microbiomes were less mature in the after-pandemic cohort than in the before-pandemic cohort in the children group (3-12 years old) and had features of a significantly younger age (average of 1.86 years). Lastly, body weight and height were significantly lower in the after-pandemic cohort than in the before-pandemic cohort in infants (<1 year of age), which was associated with a decrease in bacterial loads in the fecal microbiome.},
}

@article {pmid38748319,
year = {2024},
author = {Eveleens Maarse, BC and Ronner, MN and Jansen, MAA and Niemeyer-van der Kolk, T and In 't Veld, AE and Klaassen, ES and Ahmad, S and Itano, A and McHale, D and Moerland, M},
title = {Immunomodulating effects of the single bacterial strain therapy EDP1815 on innate and adaptive immune challenge responses - a randomized, placebo-controlled clinical trial.},
journal = {Immunologic research},
volume = {},
number = {},
pages = {},
pmid = {38748319},
issn = {1559-0755},
abstract = {The gut microbiome can modulate systemic inflammation and is therefore target for immunomodulation. Immunomodulating effects of EDP1815, a bacterial commensal strain of Prevotella histicola, were studied in healthy participants. Effects on adaptive immunity were evaluated by a neo-antigen challenge with keyhole limpet haemocyanin (KLH), while effects on innate immunity were evaluated by topical toll-like receptor 7 (TLR7) agonist imiquimod. Capsules with two enteric coating levels (EC1, EC2) were compared. Thirty-six healthy participants were included and received a daily dose of 8 × 10[10] cells EDP1815-EC1, EDP1815-EC2 or placebo (randomization 1:1:1) for 60 days. They received KLH vaccinations at days 8, 24 and 36, with intradermal skin challenge at day 57. KLH challenge outcomes were antibody levels, and skin blood flow and erythema after skin challenge, measured by imaging techniques. Imiquimod administration started at day 57, for 72 h. Outcomes consisted of imaging measurements similar to the KLH challenge, and the influx of inflammatory cells and cytokines in blister fluid. There was no effect of EDP1815 treatment on the KLH challenge, neither on the imaging outcomes of the imiquimod challenge. There was a consistently lower influx of inflammatory cells in the blister fluid of EDP1815-treated participants (neutrophils, p = 0.016; granulocytes, p = 0.024), more pronounced in EC1. There was a lower influx of interleukin [IL]-1β, IL-6, IL-8, IL-10, interferon [IFN]-γ and tumour necrosis factor in blister fluid of EDP1815-treated participants. EDP1815 had immunomodulatory effects on the innate immune response driven by imiquimod, but no effect on the KLH challenge was observed. Trial registration number: NCT05682222; date: 22 July 2022.},
}

@article {pmid38747631,
year = {2024},
author = {Medeiros, W and Hidalgo, K and Leão, T and de Carvalho, LM and Ziemert, N and Oliveira, V},
title = {Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0024424},
doi = {10.1128/spectrum.00244-24},
pmid = {38747631},
issn = {2165-0497},
abstract = {Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.},
}

@article {pmid38747618,
year = {2024},
author = {Isokääntä, H and Tomnikov, N and Vanhatalo, S and Munukka, E and Huovinen, P and Hakanen, AJ and Kallonen, T},
title = {High-throughput DNA extraction strategy for fecal microbiome studies.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0293223},
doi = {10.1128/spectrum.02932-23},
pmid = {38747618},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiome studies are becoming larger in size to detect the potentially small effect that environmental factors have on our gut microbiomes, or that the microbiome has on our health. Therefore, fast and reproducible DNA isolation methods are needed to handle thousands of fecal samples. We used the Chemagic 360 chemistry and Magnetic Separation Module I (MSMI) instrument to compare two sample preservatives and four different pre-treatment protocols to find an optimal method for DNA isolation from thousands of fecal samples. The pre-treatments included bead beating, sample handling in tube and plate format, and proteinase K incubation. The optimal method offers a sufficient yield of high-quality DNA without contamination. Three human fecal samples (adult, senior, and infant) with technical replicates were extracted. The extraction included negative controls (OMNIgeneGUT, DNA/RNA shield fluid, and Chemagic Lysis Buffer 1) to detect cross-contamination and ZymoBIOMICS Gut Microbiome Standard as a positive control to mimic the human gut microbiome and assess sensitivity of the extraction method. All samples were extracted using Chemagic DNA Stool 200 H96 kit (PerkinElmer, Finland). The samples were collected in two preservatives, OMNIgeneGUT and DNA/RNA shield fluid. DNA quantity was measured using Qubit-fluorometer, DNA purity and quality using gel electrophoresis, and taxonomic signatures with 16S rRNA gene-based sequencing with V3V4 and V4 regions. Bead beating increased bacterial diversity. The largest increase was detected in gram-positive genera Blautia, Bifidobacterium, and Ruminococcus. Preservatives showed minor differences in bacterial abundances. The profiles between the V3V4 and V4 regions differed considerably with lower diversity samples. Negative controls showed signs from genera abundant in fecal samples. Technical replicates of the Gut Standard and stool samples showed low variation. The selected isolation protocol included recommended steps from manufacturer as well as bead beating. Bead beating was found to be necessary to detect hard-to-lyse bacteria. The protocol was reproducible in terms of DNA yield among different stool replicates and the ZymoBIOMICS Gut Microbiome Standard. The MSM1 instrument and pre-treatment in a 96-format offered the possibility of automation and handling of large sample collections. Both preservatives were feasible in terms of sample handling and had low variation in taxonomic signatures. The 16S rRNA target region had a high impact on the composition of the bacterial profile.

IMPORTANCE: Next-generation sequencing (NGS) is a widely used method for determining the composition of the gut microbiota. Due to the differences in the gut microbiota composition between individuals, microbiome studies have expanded into large population studies to maximize detection of small effects on microbe-host interactions. Thus, the demand for a rapid and reliable microbial profiling is continuously increasing, making the optimization of high-throughput 96-format DNA extraction integral for NGS-based downstream applications. However, experimental protocols are prone to bias and errors from sample collection and storage, to DNA extraction, primer selection and sequencing, and bioinformatics analyses. Methodological bias can contribute to differences in microbiome profiles, causing variability across studies and laboratories using different protocols. To improve consistency and confidence of the measurements, the standardization of microbiome analysis methods has been recognized in many fields.},
}

@article {pmid38747616,
year = {2024},
author = {Bukavina, L and Ginwala, R and Eltoukhi, M and Sindhani, M and Prunty, M and Geynisman, DM and Ghatalia, P and Valentine, H and Calaway, A and Correa, AF and Brown, JR and Mishra, K and Plimack, ER and Kutikov, A and Ghannoum, M and Elshaer, M and Retuerto, M and Ponsky, L and Uzzo, RG and Abbosh, PH},
title = {Role of Gut Microbiome in Neoadjuvant Chemotherapy Response in Urothelial Carcinoma: A Multi-Institutional Prospective Cohort Evaluation.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-23-0479},
pmid = {38747616},
issn = {2767-9764},
abstract = {Neoadjuvant chemotherapy (NAC) is linked with clinical advantages in urothelial carcinoma for patients with muscle-invasive bladder cancer (MIBC). Despite comprehensive research into the influence of tumor mutation expression profiles and clinicopathological factors on chemotherapy response, the role of the gut microbiome (GM) in bladder cancer(BC) chemotherapy response remains poorly understood. This study examines the variance in the gut microbiome(GM) of BC patients compared to healthy adults, and investigates GM compositional differences between patients who respond to chemotherapy versus those who exhibit residual disease. Our study reveals distinct clustering, effectively separating the BC and healthy cohorts. However, no significant differences were observed between chemotherapy responders and non-responders within community subgroups. Machine Learning models based on responder status outperformed clinical variables in predicting complete response (AUC 0.88 vs AUC 0.50), although no single microbial species emerged as a fully reliable biomarker. The evaluation of short-chain fatty acid (SCFA) concentration in blood and stool revealed no correlation with responder status. Still, SCFA analysis showed a higher abundance of Akkermansia (rs = 0.51, p = 0.017) and Clostridia (rs = 0.52, p = 0.018), which correlated with increased levels of detectable fecal isobutyric acid. Higher levels of fecal Lactobacillus (rs = 0.49, p=0.02) and Enterobacteriaceae (rs = 0.52, p < 0.03) correlated with increased fecal propionic acid. In conclusion, our study constitutes the first large-scale, multi-center assessment of GM composition, suggesting the potential for a complex microbial signature to predict patients more likely to respond to NAC based on multiple taxa.},
}

@article {pmid38747598,
year = {2024},
author = {Junker, R and Valence, F and Mistou, M-Y and Chaillou, S and Chiapello, H},
title = {Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0031224},
doi = {10.1128/spectrum.00312-24},
pmid = {38747598},
issn = {2165-0497},
abstract = {UNLABELLED: The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the "stochastic block model" method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages.

IMPORTANCE: Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.},
}

@article {pmid38747597,
year = {2024},
author = {Stindt, KR and McClean, MN},
title = {Tuning interdomain conjugation to enable in situ population modification in yeasts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0005024},
doi = {10.1128/msystems.00050-24},
pmid = {38747597},
issn = {2379-5077},
abstract = {The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.},
}

@article {pmid38747583,
year = {2024},
author = {Li, C-x and Lv, M and Liu, H-y and Lin, Y-x and Pan, J-b and You, C-x and Su, J},
title = {Comparison of the upper and lower airway microbiome in early postoperative lung transplant recipients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0379123},
doi = {10.1128/spectrum.03791-23},
pmid = {38747583},
issn = {2165-0497},
abstract = {UNLABELLED: The upper and lower respiratory tract may share microbiome because they are directly continuous, and the nasal microbiome contributes partially to the composition of the lung microbiome. But little is known about the upper and lower airway microbiome of early postoperative lung transplant recipients (LTRs). Using 16S rRNA gene sequencing, we compared paired nasal swab (NS) and bronchoalveolar lavage fluid (BALF) microbiome from 17 early postoperative LTRs. The microbiome between the two compartments were significantly different in Shannon diversity and beta diversity. Four and eight core NS-associated and BALF-associated microbiome were identified, respectively. NS samples harbored more Corynebacterium, Acinetobacter, and Pseudomonas, while BALF contained more Ralstonia, Stenotrophomonas, Enterococcus, and Pedobacter. The within-subject dissimilarity was higher than the between-subject dissimilarity, indicating a greater impact of sampling sites than sampling individuals on microbial difference. There were both difference and homogeneity between NS and BALF microbiome in early postoperative LTRs. High levels of pathogens were detected in both samples, suggesting that both of them can reflect the diseases characteristics of transplanted lung. The differences between upper and lower airway microbiome mainly come from sampling sites instead of sampling individuals.

IMPORTANCE: Lung transplantation is the only therapeutic option for patients with end-stage lung disease, but its outcome is much worse than other solid organ transplants. Little is known about the NS and BALF microbiome of early postoperative LTRs. Here, we compared paired samples of the nasal and lung microbiome from 17 early postoperative LTRs and showed both difference and homogeneity between the two samples. Most of the "core" microbiome in both NS and BALF samples were recognized respiratory pathogens, suggesting that both samples can reflect the diseases characteristics of transplanted lung. We also found that the differences between upper and lower airway microbiome in early postoperative LTRs mainly come from sampling sites instead of sampling individuals.},
}

@article {pmid38747385,
year = {2024},
author = {Lei, J and Su, Y and Jian, S and Guo, X and Yuan, M and Bates, CT and Shi, ZJ and Li, J and Su, Y and Ning, D and Wu, L and Zhou, J and Yang, Y},
title = {Warming effects on grassland soil microbial communities are amplified in cool months.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae088},
pmid = {38747385},
issn = {1751-7370},
abstract = {Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (p < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.},
}

@article {pmid38747226,
year = {2024},
author = {Jitte, S and Keluth, S and Bisht, P and Wal, P and Singh, S and Murti, K and Kumar, N},
title = {Obesity and Depression: Common Link and Possible Targets.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273291985240430074053},
pmid = {38747226},
issn = {1996-3181},
abstract = {Depression is among the main causes of disability, and its protracted manifestations could make it even harder to treat metabolic diseases. Obesity is linked to episodes of depression, which is closely correlated to abdominal adiposity and impaired food quality. The present review is aimed at studying possible links between obesity and depression along with targets to disrupt it. Research output in Pubmed and Scopus were referred for writing this manuscript. Obesity and depression are related, with the greater propensity of depressed people to gain weight, resulting in poor dietary decisions and a sedentary lifestyle. Adipokines, which include adiponectin, resistin, and leptin are secretory products of the adipose tissue. These adipokines are now being studied to learn more about the connection underlying obesity and depression. Ghrelin, a gut hormone, controls both obesity and depression. Additionally, elevated ghrelin levels result in anxiolytic and antidepressant-like effects. The gut microbiota influences the metabolic functionalities of a person, like caloric processing from indigestible nutritional compounds and storage in fatty tissue, that exposes an individual to obesity, and gut microorganisms might connect to the CNS through interconnecting pathways, including neurological, endocrine, and immunological signalling systems. The alteration of brain activity caused by gut bacteria has been related to depressive episodes. Monoamines, including dopamine, serotonin, and norepinephrine, have been widely believed to have a function in emotions and appetite control. Emotional signals stimulate arcuate neurons in the hypothalamus that are directly implicated in mood regulation and eating. The peptide hormone GLP-1(glucagon-like peptide- 1) seems to have a beneficial role as a medical regulator of defective neuroinflammation, neurogenesis, synaptic dysfunction, and neurotransmitter secretion discrepancy in the depressive brain. The gut microbiota might have its action in mood and cognition regulation, in addition to its traditional involvement in GI function regulation. This review addressed the concept that obesity-related low-grade mild inflammation in the brain contributes to chronic depression and cognitive impairments.},
}

@article {pmid38747222,
year = {2024},
author = {De, S and Banerjee, S and Rakshit, P and Banerjee, S and Kumar, SKA},
title = {Unraveling the Ties: Type 2 Diabetes and Parkinson's Disease - A Nano-Based Targeted Drug Delivery Approach.},
journal = {Current diabetes reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115733998291968240429111357},
pmid = {38747222},
issn = {1875-6417},
abstract = {The link between Type 2 Diabetes (T2DM) and Parkinson's Disease (PD) dates back to the early 1960s, and ongoing research is exploring this association. PD is linked to dysregulation of dopaminergic pathways, neuroinflammation, decreased PPAR-γ coactivator 1-α, increased phosphoprotein enriched in diabetes, and accelerated α-Syn amyloid fibril production caused by T2DM. This study aims to comprehensively evaluate the T2DM-PD association and risk factors for PD in T2DM individuals. The study reviews existing literature using reputable sources like Scopus, ScienceDirect, and PubMed, revealing a significant association between T2DM and worsened PD symptoms. Genetic profiles of T2DM-PD individuals show similarities, and potential risk factors include insulin-resistance and dysbiosis of the gut-brain microbiome. Anti-diabetic drugs exhibit neuroprotective effects in PD, and nanoscale delivery systems like exosomes, micelles, and liposomes show promise in enhancing drug efficacy by crossing the Blood-Brain Barrier (BBB). Brain targeting for PD uses exosomes, micelles, liposomes, dendrimers, solid lipid nanoparticles, nano-sized polymers, and niosomes to improve medication and gene therapy efficacy. Surface modification of nanocarriers with bioactive compounds (such as angiopep, lactoferrin, and OX26) enhances α-Syn conjugation and BBB permeability. Natural exosomes, though limited, hold potential for investigating DM-PD pathways in clinical research. The study delves into the underlying mechanisms of T2DM and PD and explores current therapeutic approaches in the field of nano-based targeted drug delivery. Emphasis is placed on resolved and ongoing issues in understanding and managing both conditions.},
}

@article {pmid38747013,
year = {2024},
author = {Yang, Z and Ni, J and Sun, X and Cui, Q and Zhang, X and Zhang, M and Zhu, X and Wu, Z and Tang, C and Zhu, J and Mao, H and Liu, K and Wang, C and Xing, C and Zhu, J},
title = {The prevention effect of Limosilactobacillus reuteri on acute kidney injury by regulating gut microbiota.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.13130},
pmid = {38747013},
issn = {1348-0421},
support = {2019SWAQ05-5-4//National Key R&D Program of China/ ; BLB19J017//National Key R&D Program of China/ ; AWS18J006//National Key R&D Program of China/ ; },
abstract = {Acute kidney injury (AKI) has considerably high morbidity and mortality but we do not have proper treatment for it. There is an urgent need to develop new prevention or treatment methods. Gut microbiota has a close connection with renal diseases and has become the new therapy target for AKI. In this study, we found the oral administration of the probiotic Limosilactobacillus reuteri had a prevention effect on the AKI induced by lipopolysaccharide (LPS). It reduced serum concentration of creatinine and urea nitrogen and protected the renal cells from necrosis and apoptosis. Meanwhile, L. reuteri improved the gut barrier function, which is destroyed in AKI, and modulated the gut microbiota and relevant metabolites. Compared with the LPS group, L. reuteri increased the proportion of Proteobacteria and reduced the proportion of Firmicutes, changing the overall structure of the gut microbiota. It also influenced the fecal metabolites and changed the metabolite pathways, such as tyrosine metabolism, pentose and glucuronate interconversions, galactose metabolism, purine metabolism, and insulin resistance. These results showed that L. reuteri is a potential therapy for AKI as it helps in sustaining the gut barrier integrity and modulating gut microbiota and related metabolites.},
}

@article {pmid38746929,
year = {2024},
author = {Tibbs-Cortes, BW and Rahic-Seggerman, FM and Schmitz-Esser, S and Boggiatto, PM and Olsen, S and Putz, EJ},
title = {Corrigendum: Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1409301},
doi = {10.3389/fvets.2024.1409301},
pmid = {38746929},
issn = {2297-1769},
abstract = {[This corrects the article DOI: 10.3389/fvets.2024.1334858.].},
}

@article {pmid38746664,
year = {2024},
author = {Baniel, A and Charpentier, MJE},
title = {The social microbiome: The missing mechanism mediating the sociality-fitness nexus?.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109806},
pmid = {38746664},
issn = {2589-0042},
abstract = {In many social mammals, early social life and social integration in adulthood largely predict individual health, lifespan, and reproductive success. So far, research has mainly focused on chronic stress as the physiological mediator between social environment and fitness. Here, we propose an alternative, non-exclusive mechanism relying on microbially mediated effects: social relationships with conspecifics in early life and adulthood might strongly contribute to diversifying host microbiomes and to the transmission of beneficial microbes. In turn, more diverse and valuable microbiomes would promote pathogen resistance and optimal health and translate into lifelong fitness benefits. This mechanism relies on recent findings showing that microbiomes are largely transmitted via social routes and play a pervasive role in host development, physiology and susceptibility to pathogens. We suggest that the social transmission of microbes could explain the sociality-fitness nexus to a similar or higher extent than chronic social stress and deserves empirical studies in social mammals.},
}

@article {pmid38746546,
year = {2024},
author = {Li, H and Hu, X and Geng, X and Xiao, B and Miao, W and Xu, Z and Deng, Y and Jiang, B and Hou, Y},
title = {Competition mode and soil nutrient status shape the role of soil microbes in the diversity-invasibility relationship.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11425},
pmid = {38746546},
issn = {2045-7758},
abstract = {Understanding the relationship between plant diversity and invasibility is essential in invasion ecology. Species-rich communities are hypothesized to be more resistant to invasions than species-poor communities. However, while soil microorganisms play a crucial role in regulating this diversity-invasibility relationship, the effects of plant competition mode and soil nutrient status on their role remain unclear. To address this, we conducted a two-stage greenhouse experiment. Soils were first conditioned by growing nine native species separately in them for 1 year, then mixed in various configurations with soils conditioned using one, three, or six species, respectively. Next, we inoculated the mixed soil into sterilized substrate soil and planted the alien species Rhus typhina and native species Ailanthus altissima as test plants. We set up two competition modes (intraspecific and interspecific) and two nutrient levels (fertilization using slow-release fertilizer and nonfertilization). Under intraspecific competition, regardless of fertilization, the biomass of the alien species was higher in soil conditioned by six native species. By contrast, under interspecific competition, the biomass increased without fertilization but remained stable with fertilization in soil conditioned by six native species. Analysis of soil microbes suggests that pathogens and symbiotic fungi in diverse plant communities influenced R. typhina growth, which varied with competition mode and nutrient status. Our findings suggest that the soil microbiome is pivotal in mediating the diversity-invasibility relationship, and this influence varies according to competition mode and nutrient status.},
}

@article {pmid38746391,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: Coverage-based Analysis for Identification of Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38746391},
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}

@article {pmid38746390,
year = {2024},
author = {Nauta, KM and Gates, D and Mechan-Llontop, M and Wang, X and Nguyen, K and Isaguirre, CN and Genjdar, M and Sheldon, RD and Burton, NO},
title = {A high-throughput screening platform for discovering bacterial species and small molecules that modify animal physiology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.29.591726},
pmid = {38746390},
abstract = {The gut microbiome has been proposed to influence many aspects of animal development and physiology. However, both the specific bacterial species and the molecular mechanisms by which bacteria exert these effects are unknown in most cases. Here, we established a high throughput screening platform using the model animal Caenorhabditis elegans for identifying bacterial species and mechanisms that influence animal development and physiology. From our initial screens we found that many Bacillus species can restore normal animal development to insulin signaling mutant animals that otherwise do not develop to adulthood. To determine how Bacilli influence animal development we screened a complete non-essential gene knockout library of Bacillus subtilis for mutants that no longer restored development to adulthood. We found the Bacillus gene speB is required for animal development. In the absence of speB , B. subtilis produces excess N1-aminopropylagmatine. This polyamine is taken up by animal intestinal cells via the polyamine transporter CATP-5. When this molecule is taken up in sufficient quantities it inhibits animal mitochondrial function and causes diverse species of animals to arrest their development. To our knowledge, these are the first observations that B. subtilis can produce N1-aminopropylagmatine and that polyamines produced by intestinal microbiome species can antagonize animal development and mitochondrial function. Given that Bacilli species are regularly isolated from animal intestinal microbiomes, including from humans, we propose that altered polyamine production from intestinal Bacilli is likely to also influence animal development and metabolism in other species and potentially even contribute developmental and metabolic pathologies in humans. In addition, our findings demonstrate that C. elegans can be used as a model animal to conduct high throughput screens for bacterial species and bioactive molecules that alter animal physiology.},
}

@article {pmid38746233,
year = {2024},
author = {Hutchison, ER and Yen, MI and Peng, HW and Davis, CR and Vivas, EI and Tallon, MM and Bui, TPN and de Vos, WM and Yen, CE and Nieuwdorp, M and Rey, FE},
title = {The gut microbiome modulates the impact of Anaerobutyricum soehngenii supplementation on glucose homeostasis in mice.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4324489/v1},
pmid = {38746233},
abstract = {Background There is growing interest in the development of next-generation probiotics to prevent or treat metabolic syndrome. Previous studies suggested that Anaerobutyricum soehngenii may represent a promising probiotic candidate. A recent human study showed that while A . soehngenii supplementation is well tolerated and safe, it resulted in variable responses among individuals with a subset of the subjects significantly benefiting from the treatment. We hypothesized that gut microbiome variation is linked to the heterogeneous responses to A . soehngenii treatment observed in humans. Results We colonized germ-free mice with fecal microbiota from human subjects that responded to A . soehngenii treatment (R65 and R55) and non-responder subjects (N96 and N40). Colonized mice were fed a high-fat diet (45% kcal from fat) to induce insulin resistance, and orally treated with either live A . soehngenii culture or heat-killed culture. We found that R65-colonized mice received a benefit in glycemic control with live A . soehngenii treatment while mice colonized with microbiota from the other donors did not. The glucose homeostasis improvements observed in R65-colonized mice were positively correlated with levels of cecal propionate, an association that was reversed in N40-colonized mice. To test whether the microbiome modulates the effects of propionate, R65- or N40-colonized mice were treated with tripropionin (TP, glycerol tripropionate), a pro-drug of propionate, or glycerol (control). TP supplementation showed a similar response pattern as that observed in live A . soehngenii treatment, suggesting that propionate may mediate the effects of A . soehngenii . We also found that TP supplementation to conventional mice reduces adiposity, improves glycemic control, and reduces plasma insulin compared to control animals supplemented with glycerol. Conclusions These findings highlight the importance of the microbiome on glycemic control and underscore the need to better understand personal microbiome-by-therapeutic interactions to develop more effective treatment strategies.},
}

@article {pmid38746196,
year = {2024},
author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR},
title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.30.591865},
pmid = {38746196},
abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.

METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.

RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.

CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.},
}

@article {pmid38746008,
year = {2024},
author = {Manafu, Z and Zhang, Z and Malajiang, X and Abula, S and Guo, Q and Wu, Y and Wusiman, A and Bake, B},
title = {Effects of Alhagi camelorum Fisch polysaccharide from different regions on growth performance and gastrointestinal microbiota of sheep lambs.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1379394},
pmid = {38746008},
issn = {1663-9812},
abstract = {Polysaccharides derived from Alhagi camelorum Fisch possess diverse activities, making them a potential prebiotic candidates for enhancing lamb health. This study investigated the immunomodulatory effects of Alhagi camelorum Fisch polysaccharides from Aksu (AK) and Shanshan (SS) regions on sheep lambs. The results showed that sheep lambs in the SS group exhibited significantly increased (p < 0.05) average daily gain, levels of growth hormone (GH), insulin (INS), IgA and IgM, and cytokines IL-4, IL-10, IL-17, TNF-α and IFN-γ compared to those in the control check (CK) group. Moreover, the SS treatment significantly increased the diversity and abundance of beneficial bacteria, while concurrently diminishing the prevalence of harmful bacteria. Additionally, it modulated various metabolic pathways, promoted lamb growth, improved immunity, reduced the risk of gastrointestinal disease and improved the composition of gastrointestinal microbiota. In summary, our findings highlight the potential of SS treatment in enhancing gastrointestinal health of sheep lambs by improving intestinal function, immunity, and gut microbiome. Consequently, these results suggest that Alhagi camelorum Fisch polysaccharides derived from Shanshan regions holds promising potential as a valuable intervention for optimizing growth performance in sheep lambs.},
}

@article {pmid38745980,
year = {2024},
author = {Knobloch, S and Skirnisdóttir, S and Dubois, M and Mayolle, L and Kolypczuk, L and Leroi, F and Leeper, A and Passerini, D and Marteinsson, VÞ},
title = {The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence.},
journal = {FEMS microbes},
volume = {5},
number = {},
pages = {xtae011},
pmid = {38745980},
issn = {2633-6685},
abstract = {The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.},
}

@article {pmid38745566,
year = {2024},
author = {Falkenstein, M and Simon, MC and Mantri, A and Weber, B and Koban, L and Plassmann, H},
title = {Impact of the gut microbiome composition on social decision-making.},
journal = {PNAS nexus},
volume = {3},
number = {5},
pages = {pgae166},
pmid = {38745566},
issn = {2752-6542},
abstract = {There is increasing evidence for the role of the gut microbiome in the regulation of socio-affective behavior in animals and clinical conditions. However, whether and how the composition of the gut microbiome may influence social decision-making in health remains unknown. Here, we tested the causal effects of a 7-week synbiotic (vs. placebo) dietary intervention on altruistic social punishment behavior in an ultimatum game. Results showed that the intervention increased participants' willingness to forgo a monetary payoff when treated unfairly. This change in social decision-making was related to changes in fasting-state serum levels of the dopamine-precursor tyrosine proposing a potential mechanistic link along the gut-microbiota-brain-behavior axis. These results improve our understanding of the bidirectional role body-brain interactions play in social decision-making and why humans at times act "irrationally" according to standard economic theory.},
}

@article {pmid38745271,
year = {2024},
author = {Vázquez-González, L and Regueira-Iglesias, A and Balsa-Castro, C and Vila-Blanco, N and Tomás, I and Carreira, MJ},
title = {PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {189},
pmid = {38745271},
issn = {1471-2105},
support = {ED481A-2021//Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia/ ; IN606B-2023/005//Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia/ ; },
mesh = {*Microbiota/genetics ; *Software ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Archaea/genetics ; *DNA Primers/metabolism/genetics ; Humans ; Mouth/microbiology ; Computer Simulation ; },
abstract = {BACKGROUND: The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels.

RESULTS: As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea.

CONCLUSIONS: This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy .},
}

*Microbiota/genetics
*Software
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Archaea/genetics
*DNA Primers/metabolism/genetics
Humans
Mouth/microbiology
Computer Simulation

@article {pmid38745256,
year = {2024},
author = {Nishisaka, CS and Ventura, JP and Bais, HP and Mendes, R},
title = {Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {33},
pmid = {38745256},
issn = {2524-6372},
support = {2021/14711-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/14711-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 302147/2022-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {BACKGROUND: Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022[eps-TasA], which is defective in exopolysaccharide (EPS) and TasA protein production.

RESULTS: qPCR revealed that the B. subtilis UD1022[eps-TasA-] strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis.

CONCLUSION: This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.},
}

@article {pmid38745254,
year = {2024},
author = {Pereira, H and Chakarov, N and Hoffman, JI and Rinaud, T and Ottensmann, M and Gladow, KP and Tobias, B and Caspers, BA and Maraci, Ö and Krüger, O},
title = {Early-life factors shaping the gut microbiota of Common buzzard nestlings.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {27},
pmid = {38745254},
issn = {2524-4671},
support = {316099922//Deutsche Forschungsgemeinschaft/ ; 396780709//Deutsche Forschungsgemeinschaft/ ; 398434413//Deutsche Forschungsgemeinschaft/ ; 433069365//Deutsche Forschungsgemeinschaft/ ; 233740704//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors.

RESULTS: We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition.

CONCLUSION: Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.},
}

@article {pmid38745212,
year = {2024},
author = {Víquez-R, L and Henrich, M and Riegel, V and Bader, M and Wilhelm, K and Heurich, M and Sommer, S},
title = {A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {28},
pmid = {38745212},
issn = {2524-4671},
abstract = {The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.},
}

@article {pmid38745207,
year = {2024},
author = {Guo, J and Li, L and Cai, Y and Kang, Y},
title = {The development of probiotics and prebiotics therapy to ulcerative colitis: a therapy that has gained considerable momentum.},
journal = {Cell communication and signaling : CCS},
volume = {22},
number = {1},
pages = {268},
pmid = {38745207},
issn = {1478-811X},
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology ; *Probiotics/therapeutic use/administration & dosage ; *Prebiotics/administration & dosage ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Ulcerative colitis (UC) is increasingly common, and it is gradually become a kind of global epidemic. UC is a type of inflammatory bowel disease (IBD), and it is a lifetime recurrent disease. UC as a common disease has become a financial burden for many people and has the potential to develop into cancer if not prevented or treated. There are multiple factors such as genetic factors, host immune system disorders, and environmental factors to cause UC. A growing body of research have suggested that intestinal microbiota as an environmental factor play an important role in the occurrence and development of UC. Meanwhile, evidence to date suggests that manipulating the gut microbiome may represent effective treatment for the prevention or management of UC. In addition, the main clinical drugs to treat UC are amino salicylate and corticosteroid. These clinical drugs always have some side effects and low success rate when treating patients with UC. Therefore, there is an urgent need for safe and efficient methods to treat UC. Based on this, probiotics and prebiotics may be a valuable treatment for UC. In order to promote the wide clinical application of probiotics and prebiotics in the treatment of UC. This review aims to summarize the recent literature as an aid to better understanding how the probiotics and prebiotics contributes to UC while evaluating and prospecting the therapeutic effect of the probiotics and prebiotics in the treatment of UC based on previous publications.},
}

Humans
*Colitis, Ulcerative/therapy/microbiology
*Probiotics/therapeutic use/administration & dosage
*Prebiotics/administration & dosage
*Gastrointestinal Microbiome
Animals

@article {pmid38745153,
year = {2024},
author = {Liu, Y and Yu, J and Yang, Y and Han, B and Wang, Q and Du, S},
title = {Investigating the causal relationship of gut microbiota with GERD and BE: a bidirectional mendelian randomization.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {471},
pmid = {38745153},
issn = {1471-2164},
support = {7204303//Beijing Natural Science Foundation/ ; 7204303//Beijing Natural Science Foundation/ ; 7204303//Beijing Natural Science Foundation/ ; 7204303//Beijing Natural Science Foundation/ ; 7204303//Beijing Natural Science Foundation/ ; 7204303//Beijing Natural Science Foundation/ ; },
mesh = {*Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Gastroesophageal Reflux/microbiology ; Humans ; *Barrett Esophagus/microbiology/genetics ; Risk Factors ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Gut microbiota(GM) have been proven associated with lots of gastrointestinal diseases, but its causal relationship with Gastroesophageal reflux disease(GERD) and Barrett's esophagus(BE) hasn't been explored. We aimed to uncover the causal relation between GM and GERD/BE and potential mediators by utilizing Mendelian Randomization(MR) analysis.

METHODS: Summary statistics of GM(comprising 301 bacteria taxa and 205 metabolism pathways) were extracted from MiBioGen Consortium(N = 18,340) and Dutch Microbiome Project(N = 7,738), GERD and BE from a multitrait meta-analysis(NGERD=602,604, NBE=56,429). Bidirectional two-sample MR analysis and linkage disequilibrium score regression(LDSC) were used to explore the genetic correlation between GM and GERD/BE. Mediation MR analysis was performed for the risk factors of GERD/BE, including Body mass index(BMI), weight, type 2 diabetes, major depressive disorder(MDD), smoking initiation, alcohol consumption, and dietary intake(including carbohydrate, sugar, fat, protein intake), to detect the potential mediators between GM and GERD/BE.

RESULTS: 11 bacterial taxa and 13 metabolism pathways were found associated with GERD, and 18 taxa and 5 pathways exhibited causal relationship with BE. Mediation MR analysis suggested weight and BMI played a crucial role in these relationships. LDSC identified 1 taxon and 4 metabolism pathways related to GERD, and 1 taxon related to BE. Specie Faecalibacterium prausnitzii had a suggestive impact on both GERD(OR = 1.087, 95%CI = 1.01-1.17) and BE(OR = 1.388, 95%CI = 1.03-1.86) and LDSC had determined their correlation. Reverse MR indicated that BE impacted 10 taxa and 4 pathways.

CONCLUSIONS: This study established a causal link between gut microbiota and GERD/BE, and identified the probable mediators. It offers new insights into the role of gut microbiota in the development and progression of GERD and BE in the host.},
}

*Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Gastroesophageal Reflux/microbiology
Humans
*Barrett Esophagus/microbiology/genetics
Risk Factors
Polymorphism, Single Nucleotide

@article {pmid38745112,
year = {2024},
author = {Simeon, A and Radovanović, M and Lončar-Turukalo, T and Ceci, M and Brdar, S and Pio, G},
title = {Multi-class boosting for the analysis of multiple incomplete views on microbiome data.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {188},
pmid = {38745112},
issn = {1471-2105},
support = {CA18131//European Cooperation in Science and Technology/ ; PE00000013//Ministero dell'Università e della Ricerca/ ; PE00000013//Ministero dell'Università e della Ricerca/ ; },
mesh = {*Microbiota ; *Algorithms ; *Machine Learning ; Humans ; },
abstract = {BACKGROUND: Microbiome dysbiosis has recently been associated with different diseases and disorders. In this context, machine learning (ML) approaches can be useful either to identify new patterns or learn predictive models. However, data to be fed to ML methods can be subject to different sampling, sequencing and preprocessing techniques. Each different choice in the pipeline can lead to a different view (i.e., feature set) of the same individuals, that classical (single-view) ML approaches may fail to simultaneously consider. Moreover, some views may be incomplete, i.e., some individuals may be missing in some views, possibly due to the absence of some measurements or to the fact that some features are not available/applicable for all the individuals. Multi-view learning methods can represent a possible solution to consider multiple feature sets for the same individuals, but most existing multi-view learning methods are limited to binary classification tasks or cannot work with incomplete views.

RESULTS: We propose irBoost.SH, an extension of the multi-view boosting algorithm rBoost.SH, based on multi-armed bandits. irBoost.SH solves multi-class classification tasks and can analyze incomplete views. At each iteration, it identifies one winning view using adversarial multi-armed bandits and uses its predictions to update a shared instance weight distribution in a learning process based on boosting. In our experiments, performed on 5 multi-view microbiome datasets, the model learned by irBoost.SH always outperforms the best model learned from a single view, its closest competitor rBoost.SH, and the model learned by a multi-view approach based on feature concatenation, reaching an improvement of 11.8% of the F1-score in the prediction of the Autism Spectrum disorder and of 114% in the prediction of the Colorectal Cancer disease.

CONCLUSIONS: The proposed method irBoost.SH exhibited outstanding performances in our experiments, also compared to competitor approaches. The obtained results confirm that irBoost.SH can fruitfully be adopted for the analysis of microbiome data, due to its capability to simultaneously exploit multiple feature sets obtained through different sequencing and preprocessing pipelines.},
}

*Microbiota
*Algorithms
*Machine Learning
Humans

@article {pmid38745111,
year = {2024},
author = {Gao, W and Lin, W and Li, Q and Chen, W and Yin, W and Zhu, X and Gao, S and Liu, L and Li, W and Wu, D and Zhang, G and Zhu, R and Jiao, N},
title = {Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38745111},
issn = {1750-2799},
support = {82000536//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub (https://github.com/tjcadd2020/xMarkerFinder), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server (https://www.biosino.org/xmarkerfinder).},
}

@article {pmid38745002,
year = {2024},
author = {Flemming, A},
title = {Connecting vitamin D, the microbiome and anticancer immunity.},
journal = {Nature reviews. Immunology},
volume = {},
number = {},
pages = {},
pmid = {38745002},
issn = {1474-1741},
}

@article {pmid38744997,
year = {2024},
author = {Kiani, L},
title = {Infant microbiome predicts neurodevelopmental disorders.},
journal = {Nature reviews. Neurology},
volume = {},
number = {},
pages = {},
pmid = {38744997},
issn = {1759-4766},
}

@article {pmid38744972,
year = {2024},
author = {Carlini, DB and Winslow, SK and Cloppenborg-Schmidt, K and Baines, JF},
title = {Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11021},
pmid = {38744972},
issn = {2045-2322},
support = {Mellon Grant//American University/ ; CRC 1182 Project Z03//German Science Foundation (DFG)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Seasons ; Virginia ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome's role in winter survival is warranted.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Seasons
Virginia
Bacteria/genetics/classification/isolation & purification

@article {pmid38744959,
year = {2024},
author = {Hindson, J},
title = {Multi-omic links between gut microbiome and cardiovascular disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {38744959},
issn = {1759-5053},
}

@article {pmid38744552,
year = {2024},
author = {Konen, JM and Wu, H and Gibbons, DL},
title = {Immune checkpoint blockade resistance in lung cancer: emerging mechanisms and therapeutic opportunities.},
journal = {Trends in pharmacological sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tips.2024.04.006},
pmid = {38744552},
issn = {1873-3735},
abstract = {Immune checkpoint blockade (ICB) therapy works by inhibiting suppressive checkpoints that become upregulated after T cell activation, like PD-1/PD-L1 and CTLA-4. While the initial FDA approvals of ICB have revolutionized cancer therapies and fueled a burgeoning immuno-oncology field, more recent clinical development of new agents has been slow. Here, focusing on lung cancer, we review the latest research uncovering tumor cell intrinsic and extrinsic ICB resistance mechanisms as major hurdles to treatment efficacy and clinical progress. These include genomic and non-genomic tumor cell alterations, along with host and microenvironmental factors like the microbiome, metabolite accumulation, and hypoxia. Together, these factors can cooperate to promote immunosuppression and ICB resistance. Opportunities to prevent resistance are constantly evolving in this rapidly expanding field, with the goal of moving toward personalized immunotherapeutic regimens.},
}

@article {pmid38744286,
year = {2024},
author = {Yonatan, Y and Kahn, S and Bashan, A},
title = {Interactions-based classification of a single microbial sample.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {100775},
doi = {10.1016/j.crmeth.2024.100775},
pmid = {38744286},
issn = {2667-2375},
abstract = {To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based on the interspecific microbial relationships. We verify, using both numerical simulations as well as real and shuffled microbial profiles from the human oral cavity, that the method can classify single samples based on their interspecific interactions. By analyzing the gut microbiome of people with autistic spectrum disorder, we found that our interaction-based method can improve the classification of individual subjects based on a single microbial sample. These results demonstrate that the underlying ecological interactions can be practically utilized to facilitate microbiome-based diagnosis and precision medicine.},
}

@article {pmid38744093,
year = {2024},
author = {Kulshrestha, S and Redhu, R and Dua, R and Gupta, R and Gupta, P and Gupta, S and Narad, P and Sengupta, A},
title = {16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {109},
number = {3},
pages = {116349},
doi = {10.1016/j.diagmicrobio.2024.116349},
pmid = {38744093},
issn = {1879-0070},
abstract = {Bacterial vaginosis (BV) is a prevalent vaginal illness resulting from a disruption in the vaginal microbial equilibrium. The vaginal microbiota has been shown to have a substantial impact on the development and continuation of BV. This work utilized 16S rRNA sequence analysis of vaginal microbiome samples (Control vs BV samples) utilizing Parallel-Meta 3 to investigate the variations in microbial composition. The unique genes identified were used to determine prospective therapeutic targets and their corresponding inhibitory ligands. Further, molecular docking was conducted and then MD simulations were carried out to confirm the docking outcomes. In the BV samples, we detected several anaerobic bacteria recognized for their ability to generate biofilms, namely Acetohalobium, Anaerolineaceae, Desulfobacteraceae, and others. Furthermore, we identified Dalfopristin, Clorgyline, and Hydrazine as potential therapeutic options for the management of BV. This research provides new insights into the causes of BV and shows the potential effectiveness of novel pharmacological treatments.},
}

@article {pmid38743815,
year = {2024},
author = {Masiá, M and García, JA and García-Abellán, J and Padilla, S and Fernández-González, M and Agulló, V and Gosalbes, MJ and Ruíz-Pérez, S and Mascarell, P and Botella, A and Gutiérrez, F},
title = {Distinct gut microbiota signatures associated with progression of atherosclerosis in people living with HIV.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae243},
pmid = {38743815},
issn = {1537-6613},
abstract = {BACKGROUND: The relationship of microbiota composition dynamics and the progression of subclinical atherosclerosis in people with HIV (PWH) remains unknown.

METHODS: 96-week, prospective, longitudinal study in virologically-suppressed PWH. Carotid intima-media thickness (cIMT) measurements and stool samples were obtained at baseline, 48-week and 96-week visits. cIMT progression was defined as an increase >10% and/or detection of new carotid plaque. To profile the gut microbiome, amplification and sequencing of 16S ribosomal-RNA (V3-V4 variable regions) were carried out following the Illumina protocol. Sequencing was performed with MiSeq platform.

RESULTS: 191, 190 and 167 patients had available fecal samples for microbiome analysis at the baseline, 48- and 96-week visits, respectively. 87 (43%) participants showed atherosclerosis progression, and 54 (26.7%) presented new carotid plaque. No significant differences were observed in adjusted α-diversity indices between groups defined by cIMT progression. Beta-diversity determined through principal coordinate analysis distances showed that the groups exhibited distinct microbial profiles (PERMANOVA p-value = 0.03). Longitudinal analysis with ANCOM-BC2 adjusted for traditional cardiovascular risk factors, MSM and nadir CD4 count revealed that cIMT progression was consistently associated with Agathobacter and Ruminococcus_2, while non-progression was consistently associated with Prevotella_7.

CONCLUSION: Progression of atherosclerosis in PWH might be associated with distinctive signatures in the gut microbiota.},
}

@article {pmid38743749,
year = {2024},
author = {Weiner, CM and Khan, SE and Leong, C and Ranadive, SM and Campbell, SC and Howard, JT and Heffernan, KS},
title = {Association of enterolactone with blood pressure and hypertension risk in NHANES.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0302254},
doi = {10.1371/journal.pone.0302254},
pmid = {38743749},
issn = {1932-6203},
mesh = {Humans ; *Hypertension/epidemiology/urine ; Female ; Male ; Middle Aged ; *Blood Pressure ; *4-Butyrolactone/analogs & derivatives/urine ; *Lignans/urine ; *Nutrition Surveys ; Gastrointestinal Microbiome ; Adult ; Risk Factors ; United States/epidemiology ; },
abstract = {The gut microbiome may affect overall cardiometabolic health. Enterolactone is an enterolignan reflective of dietary lignan intake and gut microbiota composition and diversity that can be measured in the urine. The purpose of this study was to examine the association between urinary enterolactone concentration as a reflection of gut health and blood pressure/risk of hypertension in a large representative sample from the US population. This analysis was conducted using data from the National Health and Nutrition Examination Survey (NHANES) collected from January 1999 through December 2010. Variables of interest included participant characteristics (including demographic, anthropometric and social/environmental factors), resting blood pressure and hypertension history, and urinary enterolactone concentration. 10,637 participants (45 years (SE = 0.3), 51.7% (SE = 0.6%) were female) were included in analyses. In multivariable models adjusted for demographic, socioeconomic and behavioral/environmental covariates, each one-unit change in log-transformed increase in enterolactone was associated with a 0.738 point (95% CI: -0.946, -0.529; p<0.001) decrease in systolic blood pressure and a 0.407 point (95% CI: -0.575, -0.239; p<0.001) decrease in diastolic blood pressure. Moreover, in fully adjusted models, each one-unit change in log-transformed enterolactone was associated with 8.2% lower odds of hypertension (OR = 0.918; 95% CI: 0.892, 0.944; p<0.001). Urinary enterolactone, an indicator of gut microbiome health, is inversely associated with blood pressure and hypertension risk in a nationally representative sample of U.S. adults.},
}

Humans
*Hypertension/epidemiology/urine
Female
Male
Middle Aged
*Blood Pressure
*4-Butyrolactone/analogs & derivatives/urine
*Lignans/urine
*Nutrition Surveys
Gastrointestinal Microbiome
Adult
Risk Factors
United States/epidemiology

@article {pmid38743725,
year = {2024},
author = {An, R and Venkatraman, A and Binns, J and Saric, C and Rey, FE and Thibeault, SL},
title = {Age and sex-related variations in murine laryngeal microbiota.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0300672},
doi = {10.1371/journal.pone.0300672},
pmid = {38743725},
issn = {1932-6203},
mesh = {Animals ; Female ; Male ; *Larynx/microbiology ; Mice ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; Age Factors ; Aging/physiology ; Bacteria/classification/genetics ; Sex Factors ; Mice, Inbred C57BL ; },
abstract = {The larynx undergoes significant age and sex-related changes in structure and function across the lifespan. Emerging evidence suggests that laryngeal microbiota influences immunological processes. Thus, there is a critical need to delineate microbial mechanisms that may underlie laryngeal physiological and immunological changes. As a first step, the present study explored potential age and sex-related changes in the laryngeal microbiota across the lifespan in a murine model. We compared laryngeal microbial profiles of mice across the lifespan (adolescents, young adults, older adults and elderly) to determine age and sex-related microbial variation on 16s rRNA gene sequencing. Measures of alpha diversity and beta diversity were obtained, along with differentially abundant taxa across age groups and biological sexes. There was relative stability of the laryngeal microbiota within each age group and no significant bacterial compositional shift in the laryngeal microbiome across the lifespan. There was an abundance of short-chain fatty acid producing bacteria in the adolescent group, unique to the laryngeal microbiota; taxonomic changes in the elderly resembled that of the aged gut microbiome. There were no significant changes in the laryngeal microbiota relating to biological sex. This is the first study to report age and sex-related variation in laryngeal microbiota. This data lays the groundwork for defining how age-related microbial mechanisms may govern laryngeal health and disease. Bacterial compositional changes, as a result of environmental or systemic stimuli, may not only be indicative of laryngeal-specific metabolic and immunoregulatory processes, but may precede structural and functional age-related changes in laryngeal physiology.},
}

Animals
Female
Male
*Larynx/microbiology
Mice
*Microbiota
*RNA, Ribosomal, 16S/genetics
Age Factors
Aging/physiology
Bacteria/classification/genetics
Sex Factors
Mice, Inbred C57BL

@article {pmid38743661,
year = {2024},
author = {Ye, W and Wu, W and Jiang, L and Yuan, C and Huang, Y and Chen, Z and Huang, Q and Qian, L},
title = {Effects of dietary phytosterols or phytosterol esters supplementation on growth performance, biochemical blood indices and intestinal flora of C57BL/6 mice.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0297788},
doi = {10.1371/journal.pone.0297788},
pmid = {38743661},
issn = {1932-6203},
mesh = {Animals ; *Phytosterols/pharmacology/administration & dosage ; *Dietary Supplements ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Liver/metabolism/drug effects ; Esters/pharmacology ; Male ; Cholesterol/blood ; Triglycerides/blood ; Animal Feed/analysis ; Superoxide Dismutase/metabolism/blood ; },
abstract = {This study was conducted to evaluate the effects of phytosterols (PS) and phytosterol esters (PSE) on C57BL/6 mice. Three groups of 34 six-week-old C57BL/6 mice of specific pathogen free (SPF) grade, with an average initial body weight (IBW) of 17.7g, were fed for 24 days either natural-ingredient diets without supplements or diets supplemented with 89 mg/kg PS or diets supplemented with 400 mg/kg PSE. Growth performance, blood biochemistry, liver and colon morphology as well as intestinal flora status were evaluated. Both PS and PSE exhibited growth promotion and feed digestibility in mice. In blood biochemistry, the addition of both PS and PSE to the diet resulted in a significant decrease in Total Cholesterol (TC) and Triglyceride (TG) levels and an increase in Superoxide Dismutase (SOD) activity. No significant changes in liver and intestinal morphology were observed. Both increased the level of Akkermansia in the intestinal tract of mice. There was no significant difference between the effects of PS and PSE. It was concluded that dietary PS and PSE supplementation could improve growth performance, immune performance and gut microbiome structure in mice, providing insights into its application as a potential feed additive in animals production.},
}

Animals
*Phytosterols/pharmacology/administration & dosage
*Dietary Supplements
*Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
Mice
*Liver/metabolism/drug effects
Esters/pharmacology
Male
Cholesterol/blood
Triglycerides/blood
Animal Feed/analysis
Superoxide Dismutase/metabolism/blood

@article {pmid38743428,
year = {2024},
author = {Chotirmall, SH and Mac Aogáin, M and Tiew, PY and Jaggi, TK and Narayana, JK and Singh, S and Hansbro, PM and Segal, LN},
title = {Targeting respiratory microbiomes in COPD and bronchiectasis.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2024.2355155},
pmid = {38743428},
issn = {1747-6356},
abstract = {INTRODUCTION: This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology and treatment outcomes.

AREAS COVERED: We detail the dynamics of the airway microbiome, its influence in chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline searches between Jan 2010 and March 2024 were retrieved and summarized. The review examines clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, anti-inflammatories and antimicrobial strategies are discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management.

EXPERT OPINION: Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogen-centric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving cross-disciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials and therapeutic development pipelines.},
}

@article {pmid38743252,
year = {2024},
author = {Chmielińska, M and Felis-Giemza, A and Olesińska, M and Paradowska-Gorycka, A and Szukiewicz, D},
title = {The failure of biological treatment in axial spondyloarthritis is linked to the factors related to increased intestinal permeability and dysbiosis: prospective observational cohort study.},
journal = {Rheumatology international},
volume = {},
number = {},
pages = {},
pmid = {38743252},
issn = {1437-160X},
abstract = {BACKGROUND: A significant number of patients with axial spondyloarthritis (axSpA) do not respond to biological therapy. Therefore, we decided to investigate the specificity of this group of patients and, in particular, whether haptoglobin (Hp), its polymorphism and zonulin, in addition to other clinical features, are predictors of poor response to biological treatment.

METHODS: 48 patients with axSpA who were unsuccessfully treated with standard drugs were converted to biological treatment, and from this time on, a 12-week follow-up was started to assess the failure of biological treatment (Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) decrease < 2 points). Predictors of treatment failure were identified using logistic regression analysis.

RESULTS: 21% of subjects had biological treatment failure. Patients who had a higher zonulin level, a history of frequent infections, were older, had inflammatory bowel disease (IBD), had a lower Hp level at the time of inclusion in biological therapy showed an increased risk of treatment failure.

CONCLUSIONS: The results of the study support the hypothesis that the effectiveness of biological treatment of axSpA is limited by changed microbiota and intestinal epithelial barrier dysfunction, as an increased risk of biological treatment failure was observed in patients who were older, had higher zonulin level, IBD and repeated courses of antibiotics due to frequent infections. Therefore, starting biological treatment should be followed by reducing intestinal permeability and regulating the disturbed gut microbiome.},
}

@article {pmid38743245,
year = {2024},
author = {de Moraes, DC and Rollin-Pinheiro, R and Pinto, MDCFR and Domingos, LTS and Barreto-Bergter, E and Ferreira-Pereira, A},
title = {Antifungal activity of β-lapachone against a fluconazole-resistant Candida auris strain.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38743245},
issn = {1678-4405},
support = {Bolsa de Pesquisa Produtividade//Universidade Estácio de Sá/ ; Financial Code 001//CAPES/ ; },
abstract = {Candida spp. can be found in the human microbiome. However, immunocompromised patients are likely to develop invasive Candida infections, with mortality rates higher than 50%. The discovery of C. auris, a species that rapidly acquire antifungal resistance, increased the concern about Candida infections. The limited number of antifungal agents and the high incidence of resistance to them make imperative the development of new antifungal drugs. β-lapachone is a biological active naphthoquinone that displays antifungal activity against C. albicans and C. glabrata. The aim of this study was to evaluate if this substance affects C. auris growth and elucidate its mechanism of action. A fluconazole-resistant C. auris isolate was used in this study. The antifungal activity of β-lapachone was determined through microbroth dilution assays, and its mechanism of action was evaluated using fluorescent probes. Interaction with fluconazole and amphotericin B was assessed by disk diffusion assay and checkerboard. β-lapachone inhibited planktonic C. auris cell growth by 92.7%, biofilm formation by 84.9%, and decrease the metabolism of preformed biofilms by 87.1% at 100 µg/ml. At 100 µg/ml, reductions of 30% and 59% of Calcofluor White and Nile red fluorescences were observed, indicating that β-lapachone affects cell wall chitin and neutral lipids content, respectively. Also, the ratio 590 nm/529 nm of JC-1 decreased 52%, showing that the compound affects mitochondria. No synergism was observed between β-lapachone and fluconazole or amphotericin B. Data show that β-lapachone may be a promising candidate to be used as monotherapy to treat C. auris resistant infections.},
}

@article {pmid38743047,
year = {2024},
author = {Namasivayam, S and Tilves, C and Ding, H and Wu, S and Domingue, JC and Ruiz-Bedoya, C and Shah, A and Bohrnsen, E and Schwarz, B and Bacorn, M and Chen, Q and Levy, S and Dominguez Bello, MG and Jain, SK and Sears, CL and Mueller, NT and Hourigan, SK},
title = {Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2353394},
pmid = {38743047},
issn = {1949-0984},
mesh = {Animals ; Humans ; Female ; Mice ; *Adiposity ; *Gastrointestinal Microbiome ; Male ; *Vagina/microbiology ; *Fecal Microbiota Transplantation ; *Feces/microbiology/chemistry ; Double-Blind Method ; Intra-Abdominal Fat/metabolism ; Infant ; Infant, Newborn ; },
abstract = {Exposing C-section infants to the maternal vaginal microbiome, coined "vaginal seeding", partially restores microbial colonization. However, whether vaginal seeding decreases metabolic disease risk is unknown. Therefore, we assessed the effect of vaginal seeding of human infants on adiposity in a murine model. Germ-free mice were colonized with transitional stool from human infants who received vaginal seeding or control (placebo) seeding in a double-blind randomized trial. There was a reduction in intraabdominal adipose tissue (IAAT) volume in male mice that received stool from vaginally seeded infants compared to control infants. Higher levels of isoleucine and lower levels of nucleic acid metabolites were observed in controls and correlated with increased IAAT. This suggests that early changes in the gut microbiome and metabolome caused by vaginal seeding have a positive impact on metabolic health.},
}

Animals
Humans
Female
Mice
*Adiposity
*Gastrointestinal Microbiome
Male
*Vagina/microbiology
*Fecal Microbiota Transplantation
*Feces/microbiology/chemistry
Double-Blind Method
Intra-Abdominal Fat/metabolism
Infant
Infant, Newborn

@article {pmid38743045,
year = {2024},
author = {Panigrahi, P},
title = {The neonatal gut microbiome and global health.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2352175},
pmid = {38743045},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Newborn ; *Global Health ; Enterocolitis, Necrotizing/microbiology/prevention & control ; Infant ; Synbiotics/administration & dosage ; Neonatal Sepsis/microbiology/prevention & control ; },
abstract = {The role of gut microbiome in health, a century-old concept, has been on the center stage of medical research recently. While different body sites, disease conditions, and populations have been targeted, neonatal and early infancy appear to be the most suitable period for such interventions. It is intriguing to note that, unlike traditional use in diarrhea and maintenance of gastrointestinal health, microbiome-mediating therapies have now addressed the most serious medical conditions in young infants such as necrotizing enterocolitis and neonatal sepsis. Unfortunately, almost all new endeavors in this space have been carried out in the Western world leaving behind millions of neonates that can benefit from such manipulations while serving as a large resource for further learning. In this review, an attempt has been made to quantify the global burden of neonatal morbidity and mortality, examples presented on interventions that have failed as a result of drawing from studies conducted in the West, and a case made for manipulating the neonatal gut microbiome to address the biggest killers in early life. A brief comparative analysis has been made to demonstrate the differences in the gut microbiota of North and South and a large clinical trial of synbiotics conducted by our group in a South Asian setting has been presented. Although challenging, the value of conducting such global health research is introduced with an intent to invite medical scientists to engage in well-planned, scientifically robust research endeavors. This can bring about innovation while saving and serving the most vulnerable citizens now and protecting them from the negative health consequences in the later part of their lives, ultimately shaping a resilient and equitable world as pledged by 193 United Nations member countries in 2015.},
}

Humans
*Gastrointestinal Microbiome
Infant, Newborn
*Global Health
Enterocolitis, Necrotizing/microbiology/prevention & control
Infant
Synbiotics/administration & dosage
Neonatal Sepsis/microbiology/prevention & control

@article {pmid38742910,
year = {2024},
author = {Shi, Z and Lan, Y and Wang, Y and Yan, X and Ma, X and Hassan, F-u and Rushdi, HE and Xu, Z and Wang, W and Deng, T},
title = {Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0134823},
doi = {10.1128/msystems.01348-23},
pmid = {38742910},
issn = {2379-5077},
abstract = {Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.},
}

@article {pmid38742892,
year = {2024},
author = {Martyn, C and Hayes, BM and Lauko, D and Midthun, E and Castaneda, G and Bosco-Lauth, A and Salkeld, DJ and Kistler, A and Pollard, KS and Chou, S},
title = {Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0032124},
doi = {10.1128/msystems.00321-24},
pmid = {38742892},
issn = {2379-5077},
abstract = {UNLABELLED: Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks.

IMPORTANCE: Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.},
}

@article {pmid38742890,
year = {2024},
author = {Rodriguez, CI and Isobe, K and Martiny, JBH},
title = {Short-term dietary fiber interventions produce consistent gut microbiome responses across studies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0013324},
doi = {10.1128/msystems.00133-24},
pmid = {38742890},
issn = {2379-5077},
abstract = {UNLABELLED: The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies.

IMPORTANCE: Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.},
}

@article {pmid38742849,
year = {2024},
author = {Feng, Y and Lu, J and Jiang, J and Wang, M and Guo, K and Lin, S},
title = {Berberine: Potential preventive and therapeutic strategies for human colorectal cancer.},
journal = {Cell biochemistry and function},
volume = {42},
number = {4},
pages = {e4033},
doi = {10.1002/cbf.4033},
pmid = {38742849},
issn = {1099-0844},
support = {ZCLQ24H2901//Natural Science Foundation of Zhejiang Province/ ; GZS202002//Zhejiang Lin Shengyou Famous Traditional Chinese Medicine Expert Inheritance Studio Project/ ; 2024KY1328//Zhejiang Provincial Medicine and Health Technology Program/ ; 2024ZL712//Traditional Chinese Medicine Science and Technology Program of Zhejiang Province/ ; A20230054//Hangzhou Medical Health Science and Technology Project/ ; },
mesh = {*Berberine/pharmacology/therapeutic use ; Humans ; *Colorectal Neoplasms/prevention & control/drug therapy/pathology/metabolism ; Gastrointestinal Microbiome/drug effects ; Cell Proliferation/drug effects ; Apoptosis/drug effects ; },
abstract = {Colorectal cancer (CRC) is a common digestive tract tumor, with incidences continuing to rise. Although modern medicine has extended the survival time of CRC patients, its adverse effects and the financial burden cannot be ignored. CRC is a multi-step process and can be caused by the disturbance of gut microbiome and chronic inflammation's stimulation. Additionally, the presence of precancerous lesions is also a risk factor for CRC. Consequently, scientists are increasingly interested in identifying multi-target, safe, and economical herbal medicine and natural products. This paper summarizes berberine's (BBR) regulatory mechanisms in the occurrence and development of CRC. The findings indicate that BBR regulates gut microbiome homeostasis and controls mucosal inflammation to prevent CRC. In the CRC stage, BBR inhibits cell proliferation, invasion, and metastasis, blocks the cell cycle, induces cell apoptosis, regulates cell metabolism, inhibits angiogenesis, and enhances chemosensitivity. BBR plays a role in the overall management of CRC. Therefore, using BBR as an adjunct to CRC prevention and treatment could become a future trend in oncology.},
}

*Berberine/pharmacology/therapeutic use
Humans
*Colorectal Neoplasms/prevention & control/drug therapy/pathology/metabolism
Gastrointestinal Microbiome/drug effects
Cell Proliferation/drug effects
Apoptosis/drug effects

@article {pmid38742830,
year = {2024},
author = {Spurgeon, ME and Townsend, EC and Blaine-Sauer, S and McGregor, SM and Horswill, M and den Boon, JA and Ahlquist, P and Kalan, L and Lambert, PF},
title = {Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model.},
journal = {mBio},
volume = {},
number = {},
pages = {e0093324},
doi = {10.1128/mbio.00933-24},
pmid = {38742830},
issn = {2150-7511},
abstract = {Human papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States and are a major etiological agent of cancers in the anogenital tract and oral cavity. Growing evidence suggests changes in the host microbiome are associated with the natural history and ultimate outcome of HPV infection. We sought to define changes in the host cervicovaginal microbiome during papillomavirus infection, persistence, and pathogenesis using the murine papillomavirus (MmuPV1) cervicovaginal infection model. Cervicovaginal lavages were performed over a time course of MmuPV1 infection in immunocompetent female FVB/N mice and extracted DNA was analyzed by qPCR to track MmuPV1 viral copy number. 16S ribosomal RNA (rRNA) gene sequencing was used to determine the composition and diversity of microbial communities throughout this time course. We also sought to determine whether specific microbial communities exist across the spectrum of MmuPV1-induced neoplastic disease. We, therefore, performed laser-capture microdissection to isolate regions of disease representing all stages of neoplastic disease progression (normal, low- and high-grade dysplasia, and cancer) from female reproductive tract tissue sections from MmuPV1-infected mice and performed 16S rRNA sequencing. Consistent with other studies, we found that the natural murine cervicovaginal microbiome is highly variable across different experiments. Despite these differences in initial microbiome composition between experiments, we observed that MmuPV1 persistence, viral load, and severity of disease influenced the composition of the cervicovaginal microbiome. These studies demonstrate that papillomavirus infection can alter the cervicovaginal microbiome.IMPORTANCEHuman papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States. A subset of HPVs that infect the anogenital tract (cervix, vagina, anus) and oral cavity cause at least 5% of cancers worldwide. Recent evidence indicates that the community of microbial organisms present in the human cervix and vagina, known as the cervicovaginal microbiome, plays a role in HPV-induced cervical cancer. However, the mechanisms underlying this interplay are not well-defined. In this study, we infected the female reproductive tract of mice with a murine papillomavirus (MmuPV1) and found that key aspects of papillomavirus infection and disease influence the host cervicovaginal microbiome. This is the first study to define changes in the host microbiome associated with MmuPV1 infection in a preclinical animal model of HPV-induced cervical cancer. These results pave the way for using MmuPV1 infection models to further investigate the interactions between papillomaviruses and the host microbiome.},
}

@article {pmid38742649,
year = {2024},
author = {Serrano-Villar, S and Martínez, E},
title = {The Gut Microbiome: Another Piece in the Puzzle of HIV-Associated Atherosclerosis.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae244},
pmid = {38742649},
issn = {1537-6613},
}

@article {pmid38742484,
year = {2024},
author = {Makri, N and Ring, N and Shaw, DJ and Athinodorou, A and Robinson, V and Paterson, GK and Richardson, J and Gow, D and Nuttall, T},
title = {Cytological evaluation, culture and genomics to evaluate the microbiome in healthy rabbit external ear canals.},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.13256},
pmid = {38742484},
issn = {1365-3164},
support = {//R(D)SVS Hospital for Small Animals/ ; },
abstract = {BACKGROUND: Lop-eared rabbits may be predisposed to otitis externa (OE) as a consequence of their ear conformation. Although otoscopy, otic cytological evaluation and culture are valuable tools in dogs and cats, published data on rabbits remain lacking.

HYPOTHESIS/OBJECTIVES: This study aimed to assess the utility of otoscopy and cytological results in evaluating healthy rabbit external ear canals (EECs) and to characterise ear cytological and microbiological findings through culture techniques and metagenomic sequencing.

ANIMALS: Sixty-three otitis-free client-owned rabbits.

MATERIALS AND METHODS: All rabbits underwent otoscopy and ear cytological evaluation. In a subset of 12 rabbits, further bacterial and fungal culture, fungal DNA assessment and metagenomic sequencing were performed.

RESULTS: Otic cytological results revealed yeast in 73%, cocci in 42.9% and rods in 28.6% of healthy rabbit EECs. Compared to upright-eared rabbits, lop-eared rabbits had more discharge and more bacteria per oil immersion field. Culture isolated eight different species yet metagenomic sequencing identified 36, belonging to the Bacillota (Firmicutes), Pseudomonadota and Actinomycetota phyla. Staphylococcus were the most commonly observed species with both methods. Ten of 12 rabbits were yeast-positive on cytological evaluation with only three yielding fungal growth identified as Yarrowia (Candida) lipolytica, Eurotium echinulatum and Cystofilobasidium infirmominiatum.

Healthy rabbit EECs lack inflammatory cells yet can host yeast and bacteria, emphasising the need to evaluate cytological results alongside the clinical signs. Lop-ear anatomy may predispose to bacterial overgrowth and OE. Notably, yeasts may be present despite a negative culture.},
}

@article {pmid38742466,
year = {2024},
author = {Ge, Z and Chen, C and Chen, J and Jiang, Z and Chen, L and Wei, Y and Chen, H and He, L and Zou, Y and Long, X and Zhan, H and Wang, H and Wang, H and Lu, Y},
title = {Gut Microbiota-Derived 3-Hydroxybutyrate Blocks GPR43-Mediated IL6 Signaling to Ameliorate Radiation Proctopathy.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2306217},
doi = {10.1002/advs.202306217},
pmid = {38742466},
issn = {2198-3844},
support = {2018B020205002//Guangdong key areas R & D projects/ ; 202206080008//Guangdong key areas R & D projects/ ; 82103084//National Natural Science Foundation of China/ ; 2019021//Sun Yat-sen University Clinical Research 5010 Program/ ; E2018096//Guang Dong Cheung Kong Philanthropy Foundation/ ; SKLRD-Z-202008//The Project of The State Key Laboratory of Respiratory Disease/ ; },
abstract = {Radiation proctopathy (RP) is a common complication of radiotherapy for pelvic malignancies with high incidence. RP accompanies by microbial dysbiosis. However, how the gut microbiota affects the disease remains unclear. Here, metabolomics reveals that the fecal and serous concentrations of microbiota-derived 3-hydroxybutyrate (3HB) are significantly reduced in RP mice and radiotherapeutic patients. Moreover, the concentration of 3HB is negatively associated with the expression of proinflammatory IL6 that is increased along with the severity of radiation damage. 3HB treatment significantly downregulates IL6 expression and alleviates IL6-mediated radiation damage. Irradiated cell-fecal microbiota co-culture experiments and in vivo assays show that such a radioprotection of 3HB is mediated by GPR43. Microbiome analysis reveals that radiation leads to a distinct bacterial community compared to untreated controls, in which Akkermansia muciniphila is significantly reduced in RP mice and radiotherapeutic patients and is associated with lower 3HB concentration. Gavage of A. muciniphila significantly increases 3HB concentration, downregulates GPR43 and IL6 expression, and ameliorates radiation damage. Collectively, these results demonstrate that the gut microbiota, including A. muciniphila, induce higher concentrations of 3HB to block GPR43-mediated IL6 signaling, thereby conferring radioprotection. The findings reveal a novel implication of the gut-immune axis in radiation pathophysiology, with potential therapeutic applications.},
}

@article {pmid38742215,
year = {2024},
author = {Verma, KK and Joshi, A and Song, XP and Singh, S and Kumari, A and Arora, J and Singh, SK and Solanki, MK and Seth, CS and Li, YR},
title = {Synergistic interactions of nanoparticles and plant growth promoting rhizobacteria enhancing soil-plant systems: a multigenerational perspective.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1376214},
pmid = {38742215},
issn = {1664-462X},
abstract = {Sustainable food security and safety are major concerns on a global scale, especially in developed nations. Adverse agroclimatic conditions affect the largest agricultural-producing areas, which reduces the production of crops. Achieving sustainable food safety is challenging because of several factors, such as soil flooding/waterlogging, ultraviolet (UV) rays, acidic/sodic soil, hazardous ions, low and high temperatures, and nutritional imbalances. Plant growth-promoting rhizobacteria (PGPR) are widely employed in in-vitro conditions because they are widely recognized as a more environmentally and sustainably friendly approach to increasing crop yield in contaminated and fertile soil. Conversely, the use of nanoparticles (NPs) as an amendment in the soil has recently been proposed as an economical way to enhance the texture of the soil and improving agricultural yields. Nowadays, various research experiments have combined or individually applied with the PGPR and NPs for balancing soil elements and crop yield in response to control and adverse situations, with the expectation that both additives might perform well together. According to several research findings, interactive applications significantly increase sustainable crop yields more than PGPR or NPs alone. The present review summarized the functional and mechanistic basis of the interactive role of PGPR and NPs. However, this article focused on the potential of the research direction to realize the possible interaction of PGPR and NPs at a large scale in the upcoming years.},
}

@article {pmid38741828,
year = {2024},
author = {Boppana, K and Almansouri, NE and Bakkannavar, S and Faheem, Y and Jaiswal, A and Shergill, K and Nath, TS},
title = {Alterations in Gut Microbiota as Early Biomarkers for Predicting Inflammatory Bowel Disease Onset and Progression: A Systematic Review.},
journal = {Cureus},
volume = {16},
number = {4},
pages = {e58080},
pmid = {38741828},
issn = {2168-8184},
abstract = {Inflammatory bowel disease (IBD) is a chronic ailment impacting the digestive system, triggered by an unusual reaction of the immune system. It includes two types of diseases: ulcerative colitis and Crohn's disease. Nonetheless, the diagnosis and evaluation of disease progression in IBD are difficult due to the absence of distinct indicators. While conventional biomarkers from blood plasma and feces, such as C-reactive protein, fecal calprotectin, and S100A12, can be employed to gauge inflammation, they are not exclusive to IBD. There is a broad consensus that intestinal microorganisms significantly contribute to the onset of intestinal imbalance, a condition intimately linked with the cause and development of IBD. Numerous studies have indicated that the makeup of intestinal microorganisms varies between individuals with IBD and those who are healthy, particularly concerning the diversity of microbes and the proportional prevalence of certain bacteria. A total of 1475 records underwent examination. Following the eligibility assessment, 17 reports were considered. The final review encompassed 12 studies, as five articles were excluded due to insufficient details regarding cases, controls, and comparability. This article suggests that gut microbiota has potential biomarkers for the noninvasive evaluation of IBD activity. Recognizing the microbiome linked with disease activity paves the way for the development of a group of microbiota-derived indicators to evaluate the initiation and advancement of IBD. This article discusses whether changes in gut microbial composition can serve as early indicators of IBD onset and progression.},
}

@article {pmid38741737,
year = {2024},
author = {Wang, Z and Han, S and Xiao, Y and Zhang, Y and Ge, Y and Liu, X and Gao, J},
title = {Genetically supported causality between gut microbiota and frailty: a two-sample Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1324209},
pmid = {38741737},
issn = {1664-302X},
abstract = {BACKGROUND: A mounting body of evidence suggests a strong connection between gut microbiota and the risk of frailty. However, the question of causality remains unanswered. In this study, we employed a Mendelian randomization (MR) approach to assess potential causal relationships between gut microbiota and the risk of frailty.

MATERIALS AND METHODS: Summary statistics for the gut microbiome were obtained from a genome wide association study (GWAS) meta-analysis of the MiBioGen consortium (N = 18,340). Summary statistics for frailty were obtained from a GWAS meta-analysis, including the UK Biobank and TwinGene (N = 175,226). Our primary analysis utilized the inverse variance weighted (IVW) method. To enhance the robustness of our results, we also applied weighted median methods, MR Egger regression, and MR pleiotropy residual sum and outlier test. Finally, we conducted reverse MR analysis to investigate the potential for reverse causality.

RESULTS: IVW method identified 7 bacterial taxa nominally associated with the risk of FI. Class Bacteroidia (p = 0.033) and genus Eubacterium ruminantium group (p = 0.028) were protective against FI. In addition, class Betaproteobacteria (p = 0.042), genus Allisonella (p = 0.012), genus Bifidobacterium (p = 0.013), genus Clostridium innocuum group (p = 0.036) and genus Eubacterium coprostanoligenes group (p = 0.003) were associated with a higher risk of FI. No pleiotropy or heterogeneity were found.

CONCLUSION: The MR analysis indicates a causal relationship between specific gut microbiota and FI, offering new insights into the mechanisms underlying FI mediated by gut microbiota.},
}

@article {pmid38741734,
year = {2024},
author = {Rafie, SAA and Blentlinger, LR and Putt, AD and Williams, DE and Joyner, DC and Campa, MF and Schubert, MJ and Hoyt, KP and Horn, SP and Franklin, JA and Hazen, TC},
title = {Impact of prescribed fire on soil microbial communities in a Southern Appalachian Forest clear-cut.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1322151},
pmid = {38741734},
issn = {1664-302X},
abstract = {Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium[,] and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.},
}

@article {pmid38741135,
year = {2024},
author = {Cai, H and McLimans, CJ and Jiang, H and Chen, F and Krumholz, LR and Hambright, KD},
title = {Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {88},
pmid = {38741135},
issn = {2049-2618},
support = {Grant 2018YFA0903000//National Key Research and Development Program of China/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; BK20191508//Natural Science Foundation of Jiangsu Province of China/ ; },
mesh = {*Microcystis/genetics/metabolism/growth & development ; *Microbiota ; China ; *Lakes/microbiology ; Nutrients/metabolism ; Phototrophic Processes ; Aerobiosis ; Eutrophication ; Bacteria/classification/metabolism/genetics/isolation & purification ; Nitrogen/metabolism ; Carbon/metabolism ; },
abstract = {BACKGROUND: During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates.

RESULTS: During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria.

CONCLUSIONS: Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.},
}

*Microcystis/genetics/metabolism/growth & development
*Microbiota
China
*Lakes/microbiology
Nutrients/metabolism
Phototrophic Processes
Aerobiosis
Eutrophication
Bacteria/classification/metabolism/genetics/isolation & purification
Nitrogen/metabolism
Carbon/metabolism

@article {pmid38740909,
year = {2024},
author = {Han, S and Guiberson, ER and Li, Y and Sonnenburg, JL},
title = {High-throughput identification of gut microbiome-dependent metabolites.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38740909},
issn = {1750-2799},
support = {R01-DK085025//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-DK101674//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; F32AG062119//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5T32AI007328-35//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {A significant hurdle that has limited progress in microbiome science has been identifying and studying the diverse set of metabolites produced by gut microbes. Gut microbial metabolism produces thousands of difficult-to-identify metabolites, which present a challenge to study their roles in host biology. In recent years, mass spectrometry-based metabolomics has become one of the core technologies for identifying small metabolites. However, metabolomics expertise, ranging from sample preparation to instrument use and data analysis, is often lacking in academic labs. Most targeted metabolomics methods provide high levels of sensitivity and quantification, while they are limited to a panel of predefined molecules that may not be informative to microbiome-focused studies. Here we have developed a gut microbe-focused and wide-spectrum metabolomic protocol using liquid chromatography-mass spectrometry and bioinformatic analysis. This protocol enables users to carry out experiments from sample collection to data analysis, only requiring access to a liquid chromatography-mass spectrometry instrument, which is often available at local core facilities. By applying this protocol to samples containing human gut microbial metabolites, spanning from culture supernatant to human biospecimens, our approach enables high-confidence identification of >800 metabolites that can serve as candidate mediators of microbe-host interactions. We expect this protocol will lower the barrier to tracking gut bacterial metabolism in vitro and in mammalian hosts, propelling hypothesis-driven mechanistic studies and accelerating our understanding of the gut microbiome at the chemical level.},
}

@article {pmid38740652,
year = {2024},
author = {Varela, JL and Nikouli, E and Medina, A and Papaspyrou, S and Kormas, K},
title = {The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38740652},
issn = {1618-1905},
abstract = {The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.},
}

@article {pmid38740567,
year = {2024},
author = {Siemering, GS and Arriaga, FJ and Cagle, GA and Van Beek, JM and Freedman, ZB},
title = {Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {96},
number = {5},
pages = {e11036},
doi = {10.1002/wer.11036},
pmid = {38740567},
issn = {1554-7531},
support = {//Midwest Food Products Association/ ; //Wisconsin Cheese Makers Association/ ; //Wisconsin Department of Natural Resources/ ; },
mesh = {*Denitrification ; *Soil Microbiology ; *Cheese ; Vegetables ; Bacteria/classification/metabolism/genetics ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Soil/chemistry ; },
abstract = {The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.},
}

*Denitrification
*Soil Microbiology
*Cheese
Vegetables
Bacteria/classification/metabolism/genetics
Wastewater/chemistry
Waste Disposal, Fluid/methods
Soil/chemistry

@article {pmid38740280,
year = {2024},
author = {Huang, HL and Lin, CH and Lee, MR and Huang, WC and Sheu, CC and Cheng, MH and Lu, PL and Huang, CH and Yeh, YT and Yang, JM and Chong, IW and Liao, YC and Wang, JY},
title = {Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {107085},
doi = {10.1016/j.ijid.2024.107085},
pmid = {38740280},
issn = {1878-3511},
abstract = {OBJECTIVES: Predicting progression of nontuberculous mycobacterial lung disease (NTM-LD) remains challenging. This study evaluated whether sputum bacterial microbiome diversity can be the biomarker and provide novel insights into related phenotypes and treatment timing.

METHODS: We analyzed 126 sputum microbiomes of 126 patients with newly diagnosed NTM-LD due to Mycobacterium avium complex, M. abscessus complex, and M. kansasii between May 2020 and December 2021. Patients were followed for 2 years to determine their disease progression status. We identified consistently representative genera that differentiated the progressor and nonprogressor by using six methodologies. These genera were used to construct a prediction model using random forest with 5-fold cross validation.

RESULTS: Disease progression occurred in 49 (38.6%) patients. Compared with nonprogressors, α-diversity was lower in the progressors. Significant compositional differences existed in the β-diversity between groups (p=0.001). The prediction model for NTM-LD progression constructed using seven genera (Burkholderia, Pseudomonas, Sphingomonas, Candidatus Saccharibacteria, Phocaeicola, Pelomonas, and Phascolarctobacterium) with significantly differential abundance achieved an area under curve of 0.871.

CONCLUSIONS: Identification of the composition of sputum bacterial microbiome facilitates prediction of the course of NTM-LD, and maybe used to develop precision treatment involving modulating the respiratory microbiome composition to ameliorate NTM-LD.},
}

@article {pmid38740275,
year = {2024},
author = {Long, AR and Mortara, EL and Mendoza, BN and Fink, EC and Sacco, FX and Ciesla, MJ and Stack, TMM},
title = {Sequence similarity network analysis of drug- and dye-modifying azoreductase enzymes found in the human gut microbiome.},
journal = {Archives of biochemistry and biophysics},
volume = {},
number = {},
pages = {110025},
doi = {10.1016/j.abb.2024.110025},
pmid = {38740275},
issn = {1096-0384},
abstract = {Drug metabolism by human gut microbes is often exemplified by azo bond reduction in the anticolitic prodrug sulfasalazine. Azoreductase activity is often found in incubations with cell cultures or ex vivo gut microbiome samples and contributes to the xenobiotic metabolism of drugs and food additives. Applying metagenomic studies to personalized medicine requires knowledge of the genes responsible for sulfasalazine and other drug metabolism, and candidate genes and proteins for drug modifications are understudied. A representative gut-abundant azoreductase from Anaerotignum lactatifermentan DSM 14214 efficiently reduces sulfasalazine and another drug, phenazopyridine, but could not reduce all azo-bonded drugs in this class. We used enzyme kinetics to characterize this enzyme for its NADH-dependent reduction of these drugs and food additives and performed computational docking to provide the groundwork for understanding substrate specificity in this family. We performed an analysis of the Flavodoxin-like fold InterPro family (IPR003680) by computing a sequence similarity network to classify distinct subgroups of the family and then performed chemically-guided functional profiling to identify proteins that are abundant in the NIH Human Microbiome Project dataset. This strategy aims to reduce the number of unique azoreductases needed to characterize one protein family in the diverse set of potential drug- and dye-modifying activities found in the human gut microbiome.},
}

@article {pmid38740021,
year = {2024},
author = {Huang, P and Dong, Q and Wang, Y and Tian, Y and Wang, S and Zhang, C and Yu, L and Tian, F and Gao, X and Guo, H and Yi, S and Li, M and Liu, Y and Zhang, Q and Lu, W and Wang, G and Yang, B and Cui, S and Hua, D and Wang, X and Jiao, Y and Liu, L and Deng, Q and Ma, B and Wu, T and Zou, H and Shi, J and Zhang, H and Fan, D and Sheng, Y and Zhao, J and Tang, L and Zhang, H and Sun, W and , and Chen, W and Kong, X and Chen, L and Zhai, Q},
title = {Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100559},
doi = {10.1016/j.xgen.2024.100559},
pmid = {38740021},
issn = {2666-979X},
abstract = {The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.},
}

@article {pmid38739837,
year = {2024},
author = {Herbin, SR and Crum, H and Gens, K},
title = {Breaking the Cycle of Recurrent Clostridioides difficile Infections: A Narrative Review Exploring Current and Novel Therapeutic Strategies.},
journal = {Journal of pharmacy practice},
volume = {},
number = {},
pages = {8971900241248883},
doi = {10.1177/08971900241248883},
pmid = {38739837},
issn = {1531-1937},
abstract = {Clostridioides difficile is a toxin-producing bacteria that is a main cause of antibiotic-associated diarrhea. Clostridioides difficile infections (CDI) are associated with disruptions within the gastrointestinal (GI) microbiota which can be further exacerbated by CDI-targeted antibiotic treatment thereby causing recurrent CDI (rCDI) and compounding the burden placed on patients and the healthcare system. Treatment of rCDI consists of antibiotics which can be paired with preventative therapeutics, such as bezlotoxumab or fecal microbiota transplants (FMTs), if sustained clinical response is not obtained. Newer preventative strategies have been recently approved to assist in restoring balance within the GI system with the goal of preventing recurrent infections.},
}

@article {pmid38739809,
year = {2023},
author = {Balaji, SM},
title = {The Oral Microbiome's Impact on Systemic Health Introduction.},
journal = {Indian journal of dental research : official publication of Indian Society for Dental Research},
volume = {34},
number = {4},
pages = {349},
pmid = {38739809},
issn = {1998-3603},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; },
}

Humans
*Microbiota
*Mouth/microbiology

@article {pmid38739698,
year = {2024},
author = {Tang, WHW and Hazen, SL},
title = {Unraveling the Complex Relationship Between Gut Microbiome and Cardiovascular Diseases.},
journal = {Circulation},
volume = {149},
number = {20},
pages = {1543-1545},
pmid = {38739698},
issn = {1524-4539},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cardiovascular Diseases/microbiology/epidemiology ; Animals ; Dysbiosis ; },
}

Humans
*Gastrointestinal Microbiome
*Cardiovascular Diseases/microbiology/epidemiology
Animals
Dysbiosis

@article {pmid38739683,
year = {2024},
author = {Liu, Z and Tang, K and Zhou, Y and Liu, T and Guo, Y and Wu, D and Wang, X},
title = {Active prophages in coral-associated Halomonas capable of lateral transduction.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae085},
pmid = {38739683},
issn = {1751-7370},
abstract = {Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell-lysis accompanied by the formation of outer membrane vesicles (OMVs), and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage co-evolution in marine ecosystems.},
}

@article {pmid38739675,
year = {2024},
author = {Manickam, C and Upadhyay, AA and Woolley, G and Kroll, KW and Terry, K and Broedlow, CA and Klatt, NR and Bosinger, SE and Reeves, RK},
title = {Natural killer like B cells are a distinct but infrequent innate immune cell subset modulated by SIV infection of rhesus macaques.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1012223},
doi = {10.1371/journal.ppat.1012223},
pmid = {38739675},
issn = {1553-7374},
abstract = {Natural killer-like B (NKB) cells are unique innate immune cells expressing both natural killer (NK) and B cell receptors. As first responders to infection, they secrete IL-18 to induce a critical cascade of innate and adaptive immune cell infiltration and activation. However, limited research exists on the role of NKB cells in homeostasis and infection, largely due to incomplete and erroneous evaluations. To fill this knowledge gap, we investigated the expression of signaling and trafficking proteins, and the in situ localization and transcriptome of naïve NKB cells comparied to conventionally-defined NK and B cells, as well as modulations of these cells in SIV infection. Intracellular signaling proteins and trafficking markers were expressed differentially on naïve NKB cells, with high expression of CD62L and Syk, and low expression of CD69, α4β7, FcRg, Zap70, and CD3z, findings which were more similar to B cells than NK cells. CD20+NKG2a/c+ NKB cells were identified in spleen, mesenteric lymph nodes (MLN), colon, jejunum, and liver of naïve rhesus macaques (RM) via tissue imaging, with NKB cell counts concentrated in spleen and MLN. For the first time, single cell RNA sequencing (scRNAseq), including BCR sequencing, of sorted NKB cells confirmed that NKB cells are unique. Transcriptomic analysis of naïve splenic NKB cells by scRNAseq showed that NKB cells undergo somatic hypermutation and express Ig receptors, similar to B cells. While only 15% of sorted NKB cells showed transcript expression of both KLRC1 (NKG2A) and MS4A1 (CD20) genes, only 5% of cells expressed KLRC1, MS4A1, and IgH/IgL transcripts. We observed expanded NKB frequencies in RM gut and buccal mucosa as early as 14 and 35 days post-SIV infection, respectively. Further, mucosal and peripheral NKB cells were associated with colorectal cytokine mileu and oral microbiome changes, respectively. Our studies indicate that NKB cells gated on CD3-CD14-CD20+NKG2A/C+ cells were inclusive of transcriptomically conventional B and NK cells in addition to true NKB cells, confounding accurate phenotyping and frequency recordings that could only be resolved using genomic techniques. Although NKB cells were clearly elevated during SIV infection and associated with inflammatory changes during infection, further interrogation is necessary to acurately identify the true phenotype and significance of NKB cells in infection and inflammation.},
}

@article {pmid38739161,
year = {2024},
author = {Ekholm, J and Persson, F and de Blois, M and Modin, O and Gustavsson, DJI and Pronk, M and van Loosdrecht, MCM and Wilén, BM},
title = {Microbiome structure and function in parallel full-scale aerobic granular sludge and activated sludge processes.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {334},
pmid = {38739161},
issn = {1432-0614},
support = {17-122//Svenskt Vatten/ ; 2022-00195//Åke och Greta Lissheds stiftelse/ ; },
mesh = {*Sewage/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Bioreactors/microbiology ; Aerobiosis ; Sweden ; Glycogen/metabolism ; Ammonia/metabolism ; Nitrites/metabolism ; Nitrates/metabolism ; Phosphates/metabolism ; Water Purification/methods ; },
abstract = {Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS. KEY POINTS: • Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes. • Higher periodicity in microbial community structure in CAS compared to in AGS. • Similar functional groups between AGS and CAS but different composition and dynamics at genus level.},
}

*Sewage/microbiology
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
*Bioreactors/microbiology
Aerobiosis
Sweden
Glycogen/metabolism
Ammonia/metabolism
Nitrites/metabolism
Nitrates/metabolism
Phosphates/metabolism
Water Purification/methods

@article {pmid38739120,
year = {2024},
author = {Handley, BL and Sokana, O and Addo, KK and Wagner, J and Fookes, M and Harding-Esch, E and Marks, M and Thomson, NR and Doyle, RM},
title = {Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001234},
pmid = {38739120},
issn = {2057-5858},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Skin Ulcer/microbiology ; Ghana ; Male ; Yaws/microbiology/diagnosis ; Retrospective Studies ; Female ; Adult ; Bacteria/genetics/classification/isolation & purification ; Melanesia ; Middle Aged ; Staphylococcus/genetics/isolation & purification/classification ; Streptococcus pyogenes/genetics/isolation & purification/classification ; Arcanobacterium/genetics/isolation & purification ; Campylobacter/genetics/isolation & purification/classification ; },
abstract = {Cutaneous ulcers are common in yaws-endemic areas. Although often attributed to 'Treponema pallidum subsp. pertenue' and Haemophilus ducreyi, quantitative PCR has highlighted a significant proportion of these ulcers are negative for both pathogens and are considered idiopathic. This is a retrospective analysis utilising existing 16S rRNA sequencing data from two independent yaws studies that took place in Ghana and the Solomon Islands. We characterized bacterial diversity in 38 samples to identify potential causative agents for idiopathic cutaneous ulcers. We identified a diverse bacterial profile, including Arcanobacterium haemolyticum, Campylobacter concisus, Corynebacterium diphtheriae, Staphylococcus spp. and Streptococcus pyogenes, consistent with findings from previous cutaneous ulcer microbiome studies. No single bacterial species was universally present across all samples. The most prevalent bacterium, Campylobacter ureolyticus, appeared in 42% of samples, suggesting a multifactorial aetiology for cutaneous ulcers in yaws-endemic areas. This study emphasizes the need for a nuanced understanding of potential causative agents. The findings prompt further exploration into the intricate microbial interactions contributing to idiopathic yaw-like ulcers, guiding future research toward comprehensive diagnostic and therapeutic strategies.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Skin Ulcer/microbiology
Ghana
Male
Yaws/microbiology/diagnosis
Retrospective Studies
Female
Adult
Bacteria/genetics/classification/isolation & purification
Melanesia
Middle Aged
Staphylococcus/genetics/isolation & purification/classification
Streptococcus pyogenes/genetics/isolation & purification/classification
Arcanobacterium/genetics/isolation & purification
Campylobacter/genetics/isolation & purification/classification

@article {pmid38739117,
year = {2024},
author = {Dahlquist-Axe, G and Standeven, FJ and Speller, CF and Tedder, A and Meehan, CJ},
title = {Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001251},
pmid = {38739117},
issn = {2057-5858},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Anti-Bacterial Agents/pharmacology ; History, Ancient ; Diet ; Bacteria/genetics/classification/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; History, Medieval ; History, 17th Century ; History, 18th Century ; History, 16th Century ; },
abstract = {The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.},
}

Humans
*Microbiota
*Mouth/microbiology
*Anti-Bacterial Agents/pharmacology
History, Ancient
Diet
Bacteria/genetics/classification/drug effects
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics
History, Medieval
History, 17th Century
History, 18th Century
History, 16th Century

@article {pmid38738925,
year = {2024},
author = {Thumann, TA and Pferschy-Wenzig, E-M and Kumpitsch, C and Duller, S and Högenauer, C and Kump, P and Aziz-Kalbhenn, H and Ammar, RM and Rabini, S and Moissl-Eichinger, C and Bauer, R},
title = {Rapid biotransformation of STW 5 constituents by human gut microbiome from IBS- and non-IBS donors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0403123},
doi = {10.1128/spectrum.04031-23},
pmid = {38738925},
issn = {2165-0497},
abstract = {UNLABELLED: STW 5, a blend of nine medicinal plant extracts, exhibits promising efficacy in treating functional gastrointestinal disorders, notably irritable bowel syndrome (IBS). Nonetheless, its effects on the gastrointestinal microbiome and the role of microbiota on the conversion of its constituents are still largely unexplored. This study employed an experimental ex vivo model to investigate STW 5's differential effects on fecal microbial communities and metabolite production in samples from individuals with and without IBS. Using 560 fecal microcosms (IBS patients, n = 6; healthy controls, n = 10), we evaluated the influence of pre-digested STW 5 and controls on microbial and metabolite composition at time points 0, 0.5, 4, and 24 h. Our findings demonstrate the potential of this ex vivo platform to analyze herbal medicine turnover within 4 h with minimal microbiome shifts due to abiotic factors. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products, such as 18β-glycyrrhetinic acid, davidigenin, herniarin, 3-(3-hydroxyphenyl)propanoic acid, and 3-(2-hydroxy-4-methoxyphenyl)propanoic acid occurred. For davidigenin, 3-(3-hydroxyphenyl)propanoic acid and 18β-glycyrrhetinic acid, anti-inflammatory, cytoprotective, or spasmolytic activities have been previously described. Notably, the microbiome-driven metabolic transformation did not induce a global microbiome shift, and the detected metabolites were minimally linked to specific taxa. Observed biotransformations were independent of IBS diagnosis, suggesting potential benefits for IBS patients from biotransformation products of STW 5.

IMPORTANCE: STW 5 is an herbal medicinal product with proven clinical efficacy in the treatment of functional gastrointestinal disorders, like functional dyspepsia and irritable bowel syndrome (IBS). The effects of STW 5 on fecal microbial communities and metabolite production effects have been studied in an experimental model with fecal samples from individuals with and without IBS. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products with reported anti-inflammatory, cytoprotective, or spasmolytic activities was observed, which may be relevant for the pharmacological activity of STW 5.},
}

@article {pmid38738810,
year = {2024},
author = {Oono, R and Chou, V and Irving, M},
title = {How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13213},
pmid = {38738810},
issn = {1758-2229},
support = {DMR-1720256//Center for Scientific Computing from the CNSI, MRL: NSF MRSEC/ ; CNS-1725797//NSF/ ; //Undergraduate Research and Creative Activities Grant/ ; },
mesh = {Animals ; *Plant Leaves/microbiology ; *Herbivory ; *Asclepias/microbiology ; *Fungi/classification/genetics/isolation & purification/physiology ; Yeasts/classification/isolation & purification/genetics ; Mycobiome ; Basidiomycota/classification/genetics/physiology/isolation & purification ; Gastrointestinal Microbiome ; Larva/microbiology ; Moths/microbiology ; },
abstract = {Since a significant proportion of plant matter is consumed by herbivores, a necessary adaptation for many phyllosphere microbes could be to survive through the guts of herbivores. While many studies explore the gut microbiome of herbivores by surveying the microbiome in their frass, few studies compare the phyllosphere microbiome to the gut microbiome of herbivores. High-throughput metabarcode sequencing was used to track the fungal community from milkweed (Asclepias spp.) leaves to monarch caterpillar frass. The most commonly identified fungal taxa that dominated the caterpillar frass after the consumption of leaves were yeasts, mostly belonging to the Basidiomycota phylum. While most fungal communities underwent significant bottlenecks and some yeast taxa increased in relative abundance, a consistent directional change in community structure was not identified from leaf to caterpillar frass. These results suggest that some phyllosphere fungi, especially diverse yeasts, can survive herbivory, but whether herbivory is a key stage of their life cycle remains uncertain. For exploring phyllosphere fungi and the potential coprophilous lifestyles of endophytic and epiphytic fungi, methods that target yeast and Basidiomycota fungi are recommended.},
}

Animals
*Plant Leaves/microbiology
*Herbivory
*Asclepias/microbiology
*Fungi/classification/genetics/isolation & purification/physiology
Yeasts/classification/isolation & purification/genetics
Mycobiome
Basidiomycota/classification/genetics/physiology/isolation & purification
Gastrointestinal Microbiome
Larva/microbiology
Moths/microbiology

@article {pmid38738780,
year = {2024},
author = {An, R and Wilms, E and Gerritsen, J and Kim, HK and Pérez, CS and Besseling-van der Vaart, I and Jonkers, DMAE and Rijkers, GT and de Vos, WM and Masclee, AAM and Zoetendal, EG and Troost, FJ and Smidt, H},
title = {Spatio-temporal dynamics of the human small intestinal microbiome and its response to a synbiotic.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2350173},
pmid = {38738780},
issn = {1949-0984},
mesh = {Humans ; *Synbiotics/administration & dosage ; *Gastrointestinal Microbiome/physiology ; Male ; Adult ; *Intestine, Small/microbiology/metabolism ; Female ; *Bacteria/classification/isolation & purification/metabolism/genetics ; *Feces/microbiology ; Young Adult ; Probiotics/administration & dosage ; Metabolome ; Healthy Volunteers ; Spatio-Temporal Analysis ; },
abstract = {Although fecal microbiota composition is considered to preserve relevant and representative information for distal colonic content, it is evident that it does not represent microbial communities inhabiting the small intestine. Nevertheless, studies investigating the human small intestinal microbiome and its response to dietary intervention are still scarce. The current study investigated the spatio-temporal dynamics of the small intestinal microbiome within a day and over 20 days, as well as its responses to a 14-day synbiotic or placebo control supplementation in 20 healthy subjects. Microbial composition and metabolome of luminal content of duodenum, jejunum, proximal ileum and feces differed significantly from each other. Additionally, differences in microbiota composition along the small intestine were most pronounced in the morning after overnight fasting, whereas differences in composition were not always measurable around noon or in the afternoon. Although overall small intestinal microbiota composition did not change significantly within 1 day and during 20 days, remarkable, individual-specific temporal dynamics were observed in individual subjects. In response to the synbiotic supplementation, only the microbial diversity in jejunum changed significantly. Increased metabolic activity of probiotic strains during intestinal passage, as assessed by metatranscriptome analysis, was not observed. Nevertheless, synbiotic supplementation led to a short-term spike in the relative abundance of genera included in the product in the small intestine approximately 2 hours post-ingestion. Collectively, small intestinal microbiota are highly dynamic. Ingested probiotic bacteria could lead to a transient spike in the relative abundance of corresponding genera and ASVs, suggesting their passage through the entire gastrointestinal tract. This study was registered to http://www.clinicaltrials.gov, NCT02018900.},
}

Humans
*Synbiotics/administration & dosage
*Gastrointestinal Microbiome/physiology
Male
Adult
*Intestine, Small/microbiology/metabolism
Female
*Bacteria/classification/isolation & purification/metabolism/genetics
*Feces/microbiology
Young Adult
Probiotics/administration & dosage
Metabolome
Healthy Volunteers
Spatio-Temporal Analysis

@article {pmid38738766,
year = {2024},
author = {Wei, J and Luo, J and Yang, F and Feng, X and Zeng, M and Dai, W and Pan, X and Yang, Y and Li, Y and Duan, Y and Xiao, X and Ye, P and Yao, Z and Liu, Y and Huang, Z and Zhang, J and Zhong, Y and Xu, N and Luo, M},
title = {Cultivated Enterococcus faecium B6 from children with obesity promotes nonalcoholic fatty liver disease by the bioactive metabolite tyramine.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2351620},
pmid = {38738766},
issn = {1949-0984},
mesh = {*Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Animals ; Humans ; *Enterococcus faecium/metabolism ; Mice ; Child ; *Tyramine/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; Mice, Inbred C57BL ; Liver/metabolism/microbiology ; Pediatric Obesity/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; },
abstract = {Gut microbiota plays an essential role in nonalcoholic fatty liver disease (NAFLD). However, the contribution of individual bacterial strains and their metabolites to childhood NAFLD pathogenesis remains poorly understood. Herein, the critical bacteria in children with obesity accompanied by NAFLD were identified by microbiome analysis. Bacteria abundant in the NAFLD group were systematically assessed for their lipogenic effects. The underlying mechanisms and microbial-derived metabolites in NAFLD pathogenesis were investigated using multi-omics and LC-MS/MS analysis. The roles of the crucial metabolite in NAFLD were validated in vitro and in vivo as well as in an additional cohort. The results showed that Enterococcus spp. was enriched in children with obesity and NAFLD. The patient-derived Enterococcus faecium B6 (E. faecium B6) significantly contributed to NAFLD symptoms in mice. E. faecium B6 produced a crucial bioactive metabolite, tyramine, which probably activated PPAR-γ, leading to lipid accumulation, inflammation, and fibrosis in the liver. Moreover, these findings were successfully validated in an additional cohort. This pioneering study elucidated the important functions of cultivated E. faecium B6 and its bioactive metabolite (tyramine) in exacerbating NAFLD. These findings advance the comprehensive understanding of NAFLD pathogenesis and provide new insights for the development of microbe/metabolite-based therapeutic strategies.},
}

*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Animals
Humans
*Enterococcus faecium/metabolism
Mice
Child
*Tyramine/metabolism
*Gastrointestinal Microbiome
Male
Female
Mice, Inbred C57BL
Liver/metabolism/microbiology
Pediatric Obesity/microbiology/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification

@article {pmid38738291,
year = {2024},
author = {Liu, H},
title = {Effect of Skin Barrier on Atopic Dermatitis.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {},
number = {},
pages = {},
doi = {10.1089/derm.2024.0106},
pmid = {38738291},
issn = {2162-5220},
abstract = {The skin acts as the body's primary physical and immune barrier, maintaining the skin microbiome and providing a physical, chemical, and immune barrier. A disrupted skin barrier plays a critical role in the onset and advancement of inflammatory skin conditions such as atopic dermatitis (AD) and contact dermatitis. This narrative review outlines the relationship between AD and skin barrier function in preparation for the search for possible markers for the treatment of AD.},
}

@article {pmid38737701,
year = {2024},
author = {Lin, X and Zheng, W and Zhao, X and Zeng, M and Li, S and Peng, S and Song, T and Sun, Y},
title = {Microbiome in gynecologic malignancies: a bibliometric analysis from 2012 to 2022.},
journal = {Translational cancer research},
volume = {13},
number = {4},
pages = {1980-1996},
pmid = {38737701},
issn = {2219-6803},
abstract = {Microbiome and microbial dysbiosis have been proven to be involved in the carcinogenesis and treatment of gynecologic malignancies. However, there is a noticeable gap in the literature, as no comprehensive papers have covered general information, research status, and research frontiers in this field. This study addressed this gap by exploring the relationship between the gut and female reproductive tract (FRT) microbiome and gynecological cancers from a bibliometric perspective. Using VOSviewer 1.6.18, CiteSpace 6.1.R6, and HistCite Pro 2.1 software, we analyzed data retrieved from the Web of Science (WOS) Core Collection (WoSCC) database. Our dataset, consisting of 204 articles published from 2012 to 2022, revealed a consistent and upward publication trend. The United States and the United Kingdom were the primary driving forces, attributed to their prolificacy, high-quality output, and extensive cooperation. The University of Arizona Cancer Center, which is affiliated with the United States, ranked first among the top ten most prolific institutions. Frontiers in Cellular and Infection Microbiology emerged as the leading publisher. Herbst-Kralovetz MM led as the most productive author. Mitra A was the most influential author. Cervical cancer is notably associated with the microbiome, while endometrial and ovarian cancers are receiving increased attention in the last year. Intersections between the gut microbiome and estrogen are of growing importance. Current research focuses on identifying specific microbial species for etiological diagnosis, while frontiers mainly focus on the anticancer potential of microorganisms, such as regulating the effects of immune checkpoint inhibitors. In conclusion, this study sheds light on a novel and burgeoning direction of research, providing a one-stop overview of the microbiome in gynecologic malignancies. Its findings aim to help young researchers to identify research directions and future trends for ongoing investigations.},
}

@article {pmid38737692,
year = {2024},
author = {Sang, Y and Zheng, K and Zhao, Y and Liu, Y and Zhu, S and Xie, X and Shang, L and Liu, J and Li, L},
title = {Efficacy and regulatory strategies of gut microbiota in immunotherapy: a narrative review.},
journal = {Translational cancer research},
volume = {13},
number = {4},
pages = {2043-2063},
pmid = {38737692},
issn = {2219-6803},
abstract = {BACKGROUND AND OBJECTIVE: With advances in gut microbiome research, it has been recognized that the gut microbiome has an important and far-reaching impact on many human diseases, including cancer. Therefore, more and more researchers are focusing on the treatment of gut flora in tumors. In this article, we present a review of the mechanisms of gut microbes in tumor immunotherapy and related studies to provide reference for further research and insights into the clinical application of gut microbes.

METHODS: Between April 25, 2023, and November 25, 2023, we searched for articles published only in English between 1984 and 2023 using the databases PubMed, American Medical Association and Elsevier ScienceDirect using the keywords "gut microbiology" and "tumor" or "immunotherapy".

KEY CONTENT AND FINDINGS: The gastrointestinal tract contains the largest number of microorganisms in the human body. Microorganisms are involved in regulating many physiological activities of the body. Studies have shown that gut microbes and their derivatives are involved in the occurrence and development of a variety of inflammations and tumors, and changes in their abundance and proportion affect the degree of cancer progression and sensitivity to immunotherapy. Gut microbiota-based drug research is ongoing, and some anti-tumor studies have entered the clinical trial stage.

CONCLUSIONS: The abundance and proportion of intestinal microorganisms influence the susceptibility of tumors to tumor immunotherapy. This article reviewed the effects and mechanisms of gut microbes on tumor immunotherapy to further explore the medical value of gut microbes in tumor immunotherapy.},
}

@article {pmid38737409,
year = {2024},
author = {Scully, S and Earley, B and Smith, PE and McAloon, C and Waters, SM},
title = {Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1359611},
pmid = {38737409},
issn = {1664-302X},
abstract = {INTRODUCTION: Neonatal calf diarrhea is a multifactorial condition that occurs in early life when calves are particularly susceptible to enteric infection and dysbiosis of the gut microbiome. Good calf health is dependent on successful passive transfer of immunity from the dam through colostrum. There are limited studies on the developing gut microbiota from birth to weaning in calves.

METHODOLOGY: Therefore, the objective of this study was to examine the effect of immune status and diarrheal incidence on the development of the fecal microbiota in Jersey (n = 22) and Holstein (n = 29) heifer calves throughout the pre-weaning period. Calves were hand-fed a colostrum volume equivalent to 8.5% of their birthweight, from either the calf's dam (n = 28) or re-heated mixed colostrum (≤2 cows, ≤1d; n = 23) within 2 h of birth. All calves were clinically assessed using a modified Wisconsin-Madison calf health scoring system and rectal temperature at day (d) 0, d7, d21, or disease manifestation (DM) and weaning (d83). Weights were recorded at d0, d21, and d83. Calf blood samples were collected at d7 for the determination of calf serum IgG (sIgG). Fecal samples were obtained at d7, d21/DM [mean d22 (SE 0.70)], and at weaning for 16S rRNA amplicon sequencing of the fecal microbiota. Data were processed in R using DADA2; taxonomy was assigned using the SILVA database and further analyzed using Phyloseq and MaAsLin 2.

RESULTS AND DISCUSSION: Significant amplicon sequence variants (ASVs) and calf performance data underwent a Spearman rank-order correlation test. There was no effect (p > 0.05) of colostrum source or calf breed on serum total protein. An effect of calf breed (p < 0.05) was observed on sIgG concentrations such that Holstein calves had 6.49 (SE 2.99) mg/ml higher sIgG than Jersey calves. Colostrum source and calf breed had no effect (p > 0.05) on health status or the alpha diversity of the fecal microbiota. There was a relationship between health status and time interaction (p < 0.001), whereby alpha diversity increased with time; however, diarrheic calves had reduced microbial diversity at DM. No difference (p > 0.05) in beta diversity of the microbiota was detected at d7 or d83. At the genus level, 33 ASVs were associated (adj.p < 0.05) with health status over the pre-weaning period.},
}

@article {pmid38736850,
year = {2024},
author = {Choi, R and Bodkhe, R and Pees, B and Kim, D and Berg, M and Monnin, D and Cho, J and Narayan, V and Deller, E and Savage-Dunn, C and Shapira, M},
title = {An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome.},
journal = {Aging Biology},
volume = {2},
number = {},
pages = {},
pmid = {38736850},
support = {R01 AG061302/AG/NIA NIH HHS/United States ; R01 OD024780/OD/NIH HHS/United States ; R21 AG075315/AG/NIA NIH HHS/United States ; },
abstract = {The gut microbiome plays important roles in host function and health. Core microbiomes have been described for different species, and imbalances in their composition, known as dysbiosis, are associated with pathology. Changes in the gut microbiome and dysbiosis are common in aging, possibly due to multi-tissue deterioration, which includes metabolic shifts, dysregulated immunity, and disrupted epithelial barriers. However, the characteristics of these changes, as reported in different studies, are varied and sometimes conflicting. Using clonal populations of Caenorhabditis elegans to highlight trends shared among individuals, we employed 16s rRNA gene sequencing, CFU counts and fluorescent imaging, identifying an Enterobacteriaceae bloom as a common denominator in aging animals. Experiments using Enterobacter hormaechei, a representative commensal, suggested that the Enterobacteriaceae bloom was facilitated by a decline in Sma/BMP immune signaling in aging animals and demonstrated its potential for exacerbating infection susceptibility. However, such detrimental effects were context-dependent, mitigated by competition with commensal communities, highlighting the latter as determinants of healthy versus unhealthy aging, depending on their ability to restrain opportunistic pathobionts.},
}

@article {pmid38736752,
year = {2024},
author = {Gandasegui, J and Vergara, A and Fleitas, P and Rubio, E and Fernandez-Pittol, M and Aylagas, C and Alvarez, M and Zancada, N and Camprubí-Ferrer, D and Vila, J and Muñoz, J and Petrone, P and Casals-Pascual, C},
title = {Gut microbiota composition in travellers is associated with faecal lipocalin-2, a mediator of gut inflammation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1387126},
pmid = {38736752},
issn = {2235-2988},
mesh = {Humans ; *Lipocalin-2/metabolism ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Adult ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Diarrhea/microbiology ; Spain ; Travel ; Biomarkers ; Inflammation/microbiology ; Young Adult ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {INTRODUCTION: We examined the gut microbiota of travellers returning from tropical areas with and without traveller's diarrhoea (TD) and its association with faecal lipocalin-2 (LCN2) levels.

METHODS: Participants were recruited at the Hospital Clinic of Barcelona, Spain, and a single stool sample was collected from each individual to perform the diagnostic of the etiological agent causing gastrointestinal symptoms as well as to measure levels of faecal LCN2 as a biomarker of gut inflammation. We also characterised the composition of the gut microbiota by sequencing the region V3-V4 from the 16S rRNA gene, and assessed its relation with the clinical presentation of TD and LCN2 levels using a combination of conventional statistical tests and unsupervised machine learning approaches.

RESULTS: Among 61 participants, 45 had TD, with 40% having identifiable etiological agents. Surprisingly, LCN2 levels were similar across groups, suggesting gut inflammation occurs without clinical TD symptoms. Differential abundance (DA) testing highlighted a microbial profile tied to high LCN2 levels, marked by increased Proteobacteria and Escherichia-Shigella, and decreased Firmicutes, notably Oscillospiraceae. UMAP analysis confirmed this profile's association, revealing distinct clusters based on LCN2 levels. The study underscores the discriminatory power of UMAP in capturing meaningful microbial patterns related to clinical variables. No relevant differences in the gut microbiota composition were found between travellers with or without TD.

DISCUSSION: The findings suggest a correlation between gut microbiome and LCN2 levels during travel, emphasising the need for further research to discern the nature of this relationship.},
}

Humans
*Lipocalin-2/metabolism
*Gastrointestinal Microbiome
*Feces/microbiology/chemistry
Male
Adult
Female
*RNA, Ribosomal, 16S/genetics
Middle Aged
*Diarrhea/microbiology
Spain
Travel
Biomarkers
Inflammation/microbiology
Young Adult
Bacteria/classification/genetics/isolation & purification

@article {pmid38736461,
year = {2024},
author = {Lamont, RJ and Kuboniwa, M},
title = {The polymicrobial pathogenicity of Porphyromonas gingivalis.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1404917},
pmid = {38736461},
issn = {2673-4842},
abstract = {Accumulating microbiome data and mechanistic studies in vitro and in vivo have refined our understanding of the oral microbiota as a functionally integrated polymicrobial community. Emergent properties of these communities are driven to a large extent by interspecies communication which can be based on physical association, secreted small molecules or nutritional exchange. Porphyromonas gingivalis is a consensus periodontal pathogen; however, virulence is only expressed in the context of a polymicrobial community. Multivalent fimbriae mediate attachment to other oral species which can initiate a distinct transcriptional program in both constituents of the binding pair. P. gingivalis also responds to small molecules and nutritional cues produced by partner organisms. Physiological interdependence forms the basis of complex networks of cooperating organisms which begin to resemble an organismal entity exhibiting a spectrum of pathogenic potential.},
}

@article {pmid38736244,
year = {2024},
author = {Chen, J and Wang, X and Yang, J and Huang, J and Xie, M and Su, Z and Jiang, F},
title = {Association between gut microbiota and central retinal artery occlusion: A two-sample Mendelian randomization study.},
journal = {Indian journal of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.4103/IJO.IJO_3304_23},
pmid = {38736244},
issn = {1998-3689},
abstract = {PURPOSE: The gut microbiota might be closely related to central retinal artery occlusion (CRAO), but the causality has not been well defined. Two-sample Mendelian randomization (MR) study was used to reveal the potential causal effect between the gut microbiota and CRAO.

METHODS: Data for gut microbiota were obtained from the genome-wide association studies of the Dutch Microbiome Project (DMP) (n = 7738) and the MiBioGen consortium (n = 18,340), and data on CRAO were obtained from samples of FinnGen project (546 cases and 344,569 controls). Causalities of exposures and outcomes were explored mainly using the inverse variance weighted method. In addition, multiple sensitivity analyses including MR-Egger, weighted median (WM), simple mode, weighted mode, and MR Pleiotropy RESidual Sum and Outlier were simultaneously applied to validate the final results.

RESULTS: We identified three microbial pathways (two risk factors/one protective factor) and seven microbial taxa (two risk factors/five protective factors) associated with CRAO in the DMP study. Based on the data from the MiBioGen consortium, we identified seven microbial taxa (two risk factors/five protective factors) associated with CRAO, including the Eubacterium genus, which was consistently identified as a risk factor in both the DMP and the MiBioGen consortium MR analyses.

CONCLUSION: Our study implicates the potential causal effects of specific microbial taxa and pathways on CRAO, potentially providing new insights into the prevention and treatment of CRAO through specific gut microbial taxa and pathway. Since our conclusion is a hypothesis derived from secondary genome-wide association studies (GWAS) data analysis, further research is needed for confirmation.},
}

@article {pmid38736202,
year = {2024},
author = {Shigyo, N and Umeki, K and Hirao, T},
title = {Soil microbial identity explains home-field advantage for litter decomposition.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19769},
pmid = {38736202},
issn = {1469-8137},
support = {18J14438//Japan Society for the Promotion of Science/ ; 16K16220//Japan Society for the Promotion of Science/ ; 28-628//Japan Science Society/ ; //A joint project between the University of Tokyo Chichibu Forest and Suntory Natural Water Sanctuary/ ; },
abstract = {Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.},
}

@article {pmid38736056,
year = {2023},
author = {Singh, AK and Misra, A and Das, AK and Behl, A and Srivastava, A and Paneerselvam, A and Chidambaram, B and Saboo, B and Sethi, B and Makkar, BM and Bantwal, G and Thacker, H and Panda, J and Kesavadev, J and Seshadri, KG and Tiwaskar, M and Shunmugavelu, M and Sahay, R and Das, S and Agarwal, S and Shaikh, S and Sharma, SK and Gupta, S and Bhattacharyya, S and Mohan, V and Gunupati, VK},
title = {SGLT2i as a First-line Antihyperglycemic in the Management of Type 2 Diabetes in the Context of Indians: A Systematic Review and Consensus.},
journal = {The Journal of the Association of Physicians of India},
volume = {71},
number = {12},
pages = {62-74},
doi = {10.59556/japi.71.0422},
pmid = {38736056},
issn = {0004-5772},
mesh = {*Diabetes Mellitus, Type 2/drug therapy ; Humans ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; India ; *Hypoglycemic Agents/therapeutic use ; Consensus ; },
abstract = {BACKGROUND: Sodium-glucose cotransporter-2 inhibitors (SGLT2i) have been used for almost a decade and have proven to be effective not only in managing Type 2 diabetes (T2D), but their cardio and renal protective features make them very useful in managing patients with risk of multiple comorbidities. This systematic review was undertaken by the authors because there is no evidence currently available in India that has studied the suitability of SGLT2i as a first-line agent in patients newly diagnosed with T2D in India.

MATERIALS AND METHODS: First, literature was searched to identify features that are considered important when deciding on a first-line agent for managing T2D. A total of 5 broad topics were identified-glycemic control, extra glycemic effects, antihyperglycemic combination therapy, safety, and cost-effectiveness. These domains had further subheadings, and a total of 16 domains were identified. Metformin is the drug of choice as a first-line agent in such situations and has been considered the gold standard for evaluating the effects of SGLT2i across these domains. A systematic literature review on each domain was conducted to compare SGLT2i with the gold standard in Indian patients newly diagnosed with T2D. Evidence was graded (levels of evidence (LoE)-A, B, and C), and recommendations (class of recommendation (CoR)-I, II, and III) were classified by the expert group as defined in the methodology.

RESULTS: According to the systematic reviews conducted, 11 domains had Level A evidence, 2 domains (impact on lipids and gut microbiome) had Level B, and 3 domains had Level C (β-cell function, renal protection, and glycemic variability) evidence. Based on evidence and expert opinion, the authors recommend SGLT2i as a first-line agent for managing newly diagnosed patients with T2D with a Class I recommendation for 13 domains and Class II for the remaining 3 (impact on lipids, gut microbiome, and β-cell function). Although a poorer level of evidence (Level C) was available for the glycemic variability domain, the authors still reported this as Class I recommendations according to their expert opinion and consensus.

CONCLUSION: This article advocates adopting SGLT2 inhibitors as the primary treatment choice for treating patients with newly diagnosed T2D in India.},
}

*Diabetes Mellitus, Type 2/drug therapy
Humans
*Sodium-Glucose Transporter 2 Inhibitors/therapeutic use
India
*Hypoglycemic Agents/therapeutic use
Consensus

@article {pmid38735967,
year = {2024},
author = {Yuu, EY and Bührer, C and Eckmanns, T and Fulde, M and Herz, M and Kurzai, O and Lindstedt, C and Panagiotou, G and Piro, VC and Radonic, A and Renard, BY and Reuss, A and Siliceo, SL and Thielemann, N and Thürmer, A and Vorst, KV and Wieler, LH and Haller, S},
title = {The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {27},
pmid = {38735967},
issn = {1757-4749},
support = {H2020-MSCA-ITN-2018//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 813781 "BestTreat"//Innovative Training Networks/ ; Project NeoBIOM - 03ZZ0829A//Bundesministerium für Bildung und Forschung/ ; },
abstract = {BACKGROUND: Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing.

RESULTS: The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants.

CONCLUSIONS: Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.},
}

@article {pmid38735402,
year = {2024},
author = {Anbazhagan, AN and Ge, Y and Priyamvada, S and Kumar, A and Jayawardena, D and Palani, ARV and Husain, N and Kulkarni, N and Kapoor, S and Kaur, P and Majumder, A and Lin, YD and Maletta, L and Gill, RK and Alrefai, WA and Saksena, S and Zadeh, K and Hong, S and Mohamadzadeh, M and Dudeja, PK},
title = {A Direct Link Implicating Loss of SLC26A6 to Gut Microbial Dysbiosis, Compromised Barrier Integrity and Inflammation.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2024.05.002},
pmid = {38735402},
issn = {1528-0012},
abstract = {BACKGROUND: Putative anion transporter-1 (PAT1, SLC26A6) plays a key role in intestinal oxalate and bicarbonate secretion. PAT1 knockout (PKO) mice exhibit hyperoxaluria and nephrolithiasis. Notably, diseases such as inflammatory bowel diseases (IBD) are also associated with higher risk of hyperoxaluria and nephrolithiasis. However, the potential role of PAT1 deficiency in gut barrier integrity and susceptibility to colitis is currently elusive.

METHODS: Age-matched PKO and wild-type (WT) littermates were administered 3.5%-DSS in drinking water for 6 days. Ileum and colon of control and treated mice were harvested. mRNA and protein expression of tight junction (TJ) proteins were determined by RT-PCR and western blotting. Severity of inflammation was assessed by measuring diarrheal phenotype, cytokine expression and H&E staining. Gut microbiome and associated metabolome were analyzed by 16S rRNA sequencing and mass spectrometry, respectively.

RESULTS: PKO mice exhibited significantly higher loss of body weight, gut permeability, colonic inflammation, and diarrhea in response to DSS treatment. Additionally, PKO mice showed microbial dysbiosis and significantly reduced levels of butyrate and butyrate-producing microbes compared to controls. Cohousing WT and PKO mice for 4 weeks resulted in PKO-like signatures on the expression of TJ proteins in the colon of WT mice.

CONCLUSION: Our data demonstrate that loss of PAT1 disrupts gut microbiome and related metabolites, decreases gut barrier integrity, and increases host susceptibility to intestinal inflammation. These findings, thus, highlight a novel role of the oxalate transporter PAT1 in promoting gut barrier integrity and its deficiency appears to contribute to the pathogenesis of IBD.},
}

@article {pmid38735389,
year = {2024},
author = {Tan, X and Wu, J and Zhang, H and Li, Y and Huang, Y and Zheng, P and Xie, P},
title = {Biogeography of intestinal mucus-associated microbiome: Depletion of genus Pseudomonas is associated with depressive-like behaviors in female cynomolgus macaques.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.05.013},
pmid = {38735389},
issn = {2090-1224},
abstract = {INTRODUCTION: Depression is a debilitating and poorly understood mental disorder. There is an urgency to explore new potential biological mechanisms of depression and the gut microbiota is a promising research area.

OBJECTIVES: Our study was aim to understand regional heterogeneity and potential molecular mechanisms underlying depression induced by dysbiosis of mucus-associated microbiota.

METHODS: Here, we only selected female macaques because they are more likely to form a natural social hierarchy in a harem-like environment. Because high-ranking macaques rarely displayed depressive-like behaviors, we selected seven monkeys from high-ranking individuals as control group (HC) and the same number of low-ranking ones as depressive-like group (DL), which displayed significant depressive-like behaviors. Then, we collected mucus from the duodenum, jejunum, ileum, cecum and colon of DL and HC monkeys for shotgun metagenomic sequencing, to profile the biogeography of mucus-associated microbiota along duodenum to colon.

RESULTS: Compared with HC, DL macaques displayed noticeable depressive-like behaviors such as longer duration of huddle and sit alone behaviors (negative emotion behaviors), and fewer duration of locomotion, amicable and ingestion activities (positive emotion behaviors). Moreover, the alpha diversity index (Chao) could predict aforementioned depressive-like behaviors along duodenum to colon. Further, we identified that genus Pseudomonas was consistently decreased in DL group throughout the entire intestinal tract except for the jejunum. Specifically, there were 10, 18 and 28 decreased Pseudomonas species identified in ileum, cecum and colon, respectively. Moreover, a bacterial module mainly composed of Pseudomonas species was positively associated with three positive emotion behaviors. Functionally, Pseudomonas was mainly involved in microbiota derived lipid metabolisms such as PPAR signaling pathway, cholesterol metabolism, and fat digestion and absorption.

CONCLUSION: Different regions of intestinal mucus-associated microbiota revealed that depletion of genus Pseudomonas is associated with depressive-like behaviors in female macaques, which might induce depressive phenotypes through regulating lipid metabolism.},
}

@article {pmid38735341,
year = {2024},
author = {Zeng, Z and Tong, X and Yang, Y and Zhang, Y and Deng, S and Zhang, G and Dai, F},
title = {Pediococcus pentosaceus ZZ61 enhances growth performance and pathogenic resistance of silkworm Bombyx mori by regulating gut microbiota and metabolites.},
journal = {Bioresource technology},
volume = {402},
number = {},
pages = {130821},
doi = {10.1016/j.biortech.2024.130821},
pmid = {38735341},
issn = {1873-2976},
abstract = {Probiotics have attracted considerable attention in animal husbandry due to their positive effect on animal growth and health. This study aimed to screen candidate probiotic strain promoting the growth and health of silkworm and reveal the potential mechanisms. A novel probiotic Pediococcus pentosaceus strain (ZZ61) substantially promoted body weight gain, feed efficiency, and silk yield. These effects were likely mediated by changes in the intestinal digestive enzyme activity and nutrient provisioning (e.g., B vitamins) of the host, improving nutrient digestion and assimilation. Additionally, P. pentosaceus produced antimicrobial compounds and increased the antioxidant capacity to protect the host against pathogenic infection. Furthermore, P. pentosaceus affected the gut microbiome and altered the levels of gut metabolites (e.g., glycine and glycerophospholipids), which in turn promotes host nutrition and health. This study contributes to an improved understanding of the interactions between probiotic and host and promotes probiotic utilization in sericulture.},
}

@article {pmid38735241,
year = {2024},
author = {Huang, W and Wang, D and Zhang, XX and Zhao, M and Sun, L and Zhou, Y and Guan, X and Xie, Z},
title = {Regulatory roles of the second messenger c-di-GMP in beneficial plant-bacteria interactions.},
journal = {Microbiological research},
volume = {285},
number = {},
pages = {127748},
doi = {10.1016/j.micres.2024.127748},
pmid = {38735241},
issn = {1618-0623},
abstract = {The rhizosphere system of plants hosts a diverse consortium of bacteria that confer beneficial effects on plant, such as plant growth-promoting rhizobacteria (PGPR), biocontrol agents with disease-suppression activities, and symbiotic nitrogen fixing bacteria with the formation of root nodule. Efficient colonization in planta is of fundamental importance for promoting of these beneficial activities. However, the process of root colonization is complex, consisting of multiple stages, including chemotaxis, adhesion, aggregation, and biofilm formation. The secondary messenger, c-di-GMP (cyclic bis-(3'-5') dimeric guanosine monophosphate), plays a key regulatory role in a variety of physiological processes. This paper reviews recent progress on the actions of c-di-GMP in plant beneficial bacteria, with a specific focus on its role in chemotaxis, biofilm formation, and nodulation.},
}

@article {pmid38735183,
year = {2024},
author = {Wijaya, J and Park, J and Yang, Y and Siddiqui, SI and Oh, S},
title = {A metagenome-derived artificial intelligence modeling framework advances the predictive diagnosis and interpretation of petroleum-polluted groundwater.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134513},
doi = {10.1016/j.jhazmat.2024.134513},
pmid = {38735183},
issn = {1873-3336},
abstract = {Groundwater (GW) quality monitoring is vital for sustainable water resource management. The present study introduced a metagenome-derived machine learning (ML) model aimed at enhancing the predictive understanding and diagnostic interpretation of GW pollution associated with petroleum. In this framework, taxonomic and metabolic profiles derived from GW metagenomes were combined for use as the input dataset. By employing strategies that optimized data integration, model selection, and parameter tuning, we achieved a significant increase in diagnostic accuracy for petroleum-polluted GW. Explanatory artificial intelligence techniques identified petroleum degradation pathways and Rhodocyclaceae as strong predictors of a pollution diagnosis. Metagenomic analysis corroborated the presence of gene operons encoding aminobenzoate and xylene biodegradation within the de novo assembled genome of Rhodocyclaceae. Our genome-centric metagenomic analysis thus clarified the ecological interactions associated with microbiomes in breaking down petroleum contaminants, validating the ML-based diagnostic results. This metagenome-derived ML framework not only enhances the predictive diagnosis of petroleum pollution but also offers interpretable insights into the interaction between microbiomes and petroleum. The proposed ML framework demonstrates great promise for use as a science-based strategy for the on-site monitoring and remediation of GW pollution.},
}