@article {pmid38632404,
year = {2024},
author = {Hossain, AA and Pigli, YZ and Baca, CF and Heissel, S and Thomas, A and Libis, VK and Burian, J and Chappie, JS and Brady, SF and Rice, PA and Marraffini, LA},
title = {DNA glycosylases provide antiviral defence in prokaryotes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38632404},
issn = {1476-4687},
abstract = {Bacteria have adapted to phage predation by evolving a vast assortment of defence systems[1]. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data[2]. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library[3] with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.},
}

@article {pmid38631646,
year = {2024},
author = {Muscarella, SM and Alduina, R and Badalucco, L and Capri, FC and Di Leto, Y and Gallo, G and Laudicina, VA and Paliaga, S and Mannina, G},
title = {Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172259},
doi = {10.1016/j.scitotenv.2024.172259},
pmid = {38631646},
issn = {1879-1026},
abstract = {The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-to-bacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH.},
}

@article {pmid38631637,
year = {2024},
author = {Zhang, D and Liu, F and Al, MA and Yang, Y and Yu, H and Li, M and Wu, K and Niu, M and Wang, C and He, Z and Yan, Q},
title = {Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172518},
doi = {10.1016/j.scitotenv.2024.172518},
pmid = {38631637},
issn = {1879-1026},
abstract = {Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4[+], NO2[-] and SO4[2], while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.},
}

@article {pmid38631472,
year = {2024},
author = {Wong, MH and Minkina, T and Vasilchenko, N and Sushkova, S and Delegan, Y and Ranjan, A and Saxena, P and Tarigholizadeh, S and Dudnikova, T and Barbashev, A and Maksimov, A and Faenson, A and Kızılkaya, R},
title = {Assessment of Antibiotic Resistance Genes in Soils Polluted by Chemical and Technogenic Ways with Poly-Aromatic Hydrocarbons and Heavy Metals.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118949},
doi = {10.1016/j.envres.2024.118949},
pmid = {38631472},
issn = {1096-0953},
abstract = {Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.},
}

@article {pmid38631413,
year = {2024},
author = {Ravichandran, A and Sivapackiyam, J and Periasamy, S},
title = {Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106643},
doi = {10.1016/j.micpath.2024.106643},
pmid = {38631413},
issn = {1096-1208},
abstract = {The human oral cavity is colonized by a diverse microbial community, which includes both native and transient colonizers. The microbial composition is crucial for maintaining oral homeostasis, but due to overgrowth or imbalances of these microbial communities, dysbiosis can occur. There is a lack of understanding of the research of native and transient colonizers in the oral cavity of the Indian subpopulation Therefore, in our present study, we explored the role and prevalence of transient and native colonizers between healthy and comorbid oral diseased human individuals. Culture-dependent techniques and culture-independent 16Sr DNA metagenomic analyses were employed to isolate and study the interactions of native and transient colonizers from human oral samples. Among the 66 human individuals of both healthy and comorbid individuals, the most abundant isolate was found to be Bacillus amyloliquefaciens MCC 4424. In addition, the more prevalent culturable isolate from the healthy samples was Streptococcus salivarius MTCC 13009, whereas in comorbid samples Staphylococcus pasteuri MTCC 13076, Rothia dentocariosa MTCC 13010 and Pseudomonas aeruginosa MTCC 13077 were prevalent to a greater extent. 16S rDNA metagenomic analyses revealed the prevalence and abundance of genera such as Bacteroidetes and Proteobacteria in healthy individuals; consequently, Fusobacteria and Firmicutes were observed mostly in comorbid individuals. The significant differences in bacterial population density were observed in terms of Shannon index (p = 0.5145) and Simpson index (p = 0.9061) between the healthy and comorbid groups. B. amyloliquefaciens MCC 4424 exhibits antagonistic behavior when grown as a dual species with native and transient colonizers. This result is very consistent with the findings of antibiofilm studies using confocal laser scanning microscopy, which revealed a significant reduction in biofilm biovolume (73%) and maximum thickness (80%) and an increase in the rough coefficient of biofilms (30%). Our data suggested that B. amyloliquefaciens MCC 4424 can be a native colonizer of Indian sub-populations. It may act as a novel candidate for oral healthcare applications and greatly aids in the regulation of transient species in the oral cavity.},
}

@article {pmid38631239,
year = {2024},
author = {Yu, Y and Trottmann, NF and Schärer, MR and Fenner, K and Robinson, SL},
title = {Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater.},
journal = {Water research},
volume = {256},
number = {},
pages = {121593},
doi = {10.1016/j.watres.2024.121593},
pmid = {38631239},
issn = {1879-2448},
abstract = {Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.},
}

@article {pmid38631236,
year = {2024},
author = {Wu, H and Nie, WB and Tan, X and Xie, GJ and Qu, H and Zhang, X and Xian, Z and Dai, J and Yang, C and Chen, Y},
title = {Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss.},
journal = {Water research},
volume = {256},
number = {},
pages = {121606},
doi = {10.1016/j.watres.2024.121606},
pmid = {38631236},
issn = {1879-2448},
abstract = {Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d[-1] and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d[-1], respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.},
}

@article {pmid38631226,
year = {2024},
author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B},
title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.},
journal = {Marine environmental research},
volume = {198},
number = {},
pages = {106497},
doi = {10.1016/j.marenvres.2024.106497},
pmid = {38631226},
issn = {1879-0291},
abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.},
}

@article {pmid38632506,
year = {2024},
author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ},
title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {380},
pmid = {38632506},
issn = {1471-2164},
abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.},
}

@article {pmid38632370,
year = {2024},
author = {Sterzi, L and Nodari, R and Di Marco, F and Ferrando, ML and Saluzzo, F and Spitaleri, A and Allahverdi, H and Papaleo, S and Panelli, S and Rimoldi, SG and Batisti Biffignandi, G and Corbella, M and Cavallero, A and Prati, P and Farina, C and Cirillo, DM and Zuccotti, G and Bandi, C and Comandatore, F},
title = {Genetic barriers more than environmental associations explain Serratia marcescens population structure.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {468},
pmid = {38632370},
issn = {2399-3642},
abstract = {Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.},
}

@article {pmid38632042,
year = {2024},
author = {Coskun, ÖK and Gomez-Saez, GV and Beren, M and Özcan, D and Günay, SD and Elkin, V and Hoşgörmez, H and Einsiedl, F and Eisenreich, W and Orsi, WD},
title = {Quantifying genome specific carbon fixation in a 750 meter deep subsurface hydrothermal microbial community.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae062},
pmid = {38632042},
issn = {1574-6941},
abstract = {Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750 meter deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.},
}

@article {pmid38630611,
year = {2024},
author = {Roy, G and Prifti, E and Belda, E and Zucker, JD},
title = {Deep learning methods in metagenomics: a review.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001231},
pmid = {38630611},
issn = {2057-5858},
abstract = {The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.},
}

@article {pmid38630394,
year = {2024},
author = {Balázs, B and Boros, Á and Pankovics, P and Nagy, G and Szekeres, S and Urbán, P and Reuter, G},
title = {Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary.},
journal = {Archives of virology},
volume = {169},
number = {5},
pages = {100},
pmid = {38630394},
issn = {1432-8798},
abstract = {In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.},
}

@article {pmid38630379,
year = {2024},
author = {Sharafi, R and Salehi Jouzani, G and Karimi, E and Ghanavati, H and Kowsari, M},
title = {Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {6},
pages = {173},
pmid = {38630379},
issn = {1573-0972},
support = {2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; },
abstract = {Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg[-1] and in pilot level 65 °C, 72.11%, 310 g kg[-1]) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.},
}

@article {pmid38630153,
year = {2024},
author = {Salam, LB},
title = {Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {6},
pages = {172},
pmid = {38630153},
issn = {1573-0972},
abstract = {The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.},
}

@article {pmid38629898,
year = {2024},
author = {Li, W and He, Y and Li, Y and Li, X and Bian, T and Liu, T and Liu, X and Jiang, W},
title = {Metagenomic next-generation sequencing for the diagnosis of neurobrucellosis.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fmb-2023-0177},
pmid = {38629898},
issn = {1746-0921},
support = {XJZT19MJ21//Discipline Promotion Project of Xijing Hospital/ ; },
abstract = {Objective: This study investigates the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of neurobrucellosis (NB). Methods: We retrospectively analyzed patients diagnosed with NB who underwent cerebrospinal fluid (CSF) mNGS testing in Xijing Hospital from 2015 to 2021. Results: Among the 20 individuals included in the study, the serum rose bengal test was positive in 11 out of 16 cases, serum agglutination test was positive in 13 out of 16 cases, CSF culture was positive in 6 out of 11 cases, and CSF mNGS tests were positive in 18 out of 20 cases. Conclusion: CSF mNGS demonstrates superior sensitivity; therefore, it is recommended to collect CSF for mNGS testing prior to antibiotic therapy when NB is suspected.},
}

@article {pmid38629830,
year = {2024},
author = {Castro, AE and Montecillo, AD and Villanueva, RMD and Obusan, MCM},
title = {Bacterial community profiles of select tributaries of Laguna Lake in the Philippines.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0116123},
doi = {10.1128/mra.01161-23},
pmid = {38629830},
issn = {2576-098X},
abstract = {Laguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to be explored. We report bacterial community profiles from shotgun metagenomes of its select tributary waters.},
}

@article {pmid38629119,
year = {2024},
author = {Mason, B and Cervena, B and Frias, L and Goossens, B and Hasegawa, H and Keuk, K and Langgeng, A and Majewski, K and Matsumoto, T and Matsuura, K and Mendonça, R and Okamoto, M and Peter, S and Petrzelkova, KJ and Sipangkui, S and Xu, Z and Pafco, B and MacIntosh, AJJ},
title = {Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S0031182024000386},
pmid = {38629119},
issn = {1469-8161},
support = {15H04283//Japan Society for the Promotion of Science/ ; 16H06181//Japan Society for the Promotion of Science/ ; 20H03333//Japan Society for the Promotion of Science/ ; 24770232//Japan Society for the Promotion of Science/ ; 446//Japan Society for the Promotion of Science/ ; 22-16475S//Grantová Agentura České Republiky/ ; },
abstract = {With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.},
}

@article {pmid38628865,
year = {2024},
author = {Zhu, Q and Cui, J and Liu, S and Wei, S and Wu, Q and You, Y},
title = {Synbiotic regulates gut microbiota in patients with lupus nephritis: an analysis using metagenomic and metabolome sequencing.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1295378},
pmid = {38628865},
issn = {1664-302X},
abstract = {OBJECTIVE: To investigate the changes in gut microbes and their metabolites after administering synbiotics to patients with new-onset lupus nephritis (LN) treated using a conventional method and provide a theoretical basis for finding new targets for the diagnosis and treatment of LN.

METHODS: In this study, a total of 12 participants were divided into the lupus and synbiotic groups. Stool samples and clinical data were collected before and after treatment for metagenomic, nontargeted metabolomic, and statistical analyses.

RESULTS: The relative abundances of the pathogenic bacteria Prevotella, Bacteroides, and Enterobacteriaceae_unclassified decreased after synbiotic treatment, whereas the abundances of Actinobacteria and Firmicutes increased. Further, the Firmicutes to Bacteroidetes ratio increased; however, the difference was not statistically significant (p > 0.05). α diversity analysis showed no significant differences in the intestinal microbial richness and diversity index of patients with LN between the groups before and after treatment (p > 0.05). β analysis showed the differences in the community structure between the samples of the two groups before and after treatment. Linear discriminant analysis effect size and receiver operating characteristic curve analyses revealed that Negativicutes (AUC = 0.9722) and Enterobacteriaceae_unclassified (AUC = 0.9722) were the best predictors of the lupus and synbiotic groups, respectively, before and after treatment. Joint analyses revealed that amino acid biosynthesis, aminoacyl-tRNA biosynthesis, purine metabolism, and other metabolic pathways may be involved in the changes in the metabolic function of patients with LN after the addition of synbiotics. Spearman's correlation analysis revealed the interaction between clinical features and flora, and flora exhibited a complex biological network regulatory relationship.

CONCLUSION: Synbiotics regulate the metabolic functions of intestinal microorganisms in patients with LN and play a role in various biological functions. Synbiotic supplements may be safe and promising candidates for patients with LN.},
}

@article {pmid38628241,
year = {2024},
author = {Yuan, L and Lai, LM and Zhu, X and Rui, Z and Liu, Y and Chen, Q},
title = {Haemophilus aphrophilus and Eikenella corrodens Coinfection of Brain: An Unusual Case from China.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1439-1445},
pmid = {38628241},
issn = {1178-6973},
abstract = {BACKGROUND: The HACEK group comprises Haemophilus spp., Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae, are Gram-negative bacteria that are slow-growing and fastidious. These organisms are common causes of culture-negative endocarditis. However, brain abscesses caused by Haemophilus aphrophilus and E. corrodens have been rarely reported. The case we describe, which was promptly identified and successfully treated, will be meaningful for the diagnosis and treatment of such infectious diseases.

CASE PRESENTATION: Herein, we report a case of brain abscess in a young man who was infected with Haemophilus aphrophilus and E. corrodens. The patient was admitted to the hospital with sudden onset of vomiting, coma, and fever. Magnetic resonance imaging (MRI) of the brain and cerebrospinal fluid cell counts suggested cerebral abscess, he underwent drainage of the abscess and empirical antimicrobial therapy of meropenem (2 g every 8 hours) and linezolid (0.6 g every 12 hours) for more than 10 days without significant improvement. Metagenomic next-generation sequencing (mNGS) of drainage fluid and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) detection for isolated bacteria from samples suggested the presence of H. aphrophilus and E. corrodens. After 7 weeks of ceftriaxone (2 g every 12 hours) and meropenem (2 g every 8 hours) intravenously, the patient was discharged with a normal temperature and brain MRI showed improvement of the lesion.

CONCLUSION: Similar cases reported in previous studies were always associated with bacterial blood dissemination after dental surgery or myocarditis; however, the patient in our case had no any associated risk factors. As far as we know, this is the only case of central nervous system infection caused by H. aphrophilus and E. corrodens that has utilized combined mNGS and MALDI-TOF MS in the diagnosis.},
}

@article {pmid38628239,
year = {2024},
author = {Li, S and Han, X and Ma, J and Huang, GH and Yang, ST and Wang, CM},
title = {Study on mNGS Technique in Diagnosing Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1397-1405},
pmid = {38628239},
issn = {1178-6973},
abstract = {OBJECTIVE: To investigate the value of metagenomic Next-Generation Sequencing (mNGS) in diagnosing Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV)-infected patients.

METHODS: In this retrospective study, non-HIV-infected patients with PJP and those diagnosed with non-PJP from August 2022 to December 2024 were selected as subjects. The presence of Pneumocystis jirovecii (PJ) and other co-pathogens in bronchoalveolar lavage fluid (BALF) was analyzed, and the diagnostic efficacy of NGS, polymerase chain reaction (PCR) and serum 1,3-β-D-glucan (BDG) in PJP was compared with the reference standard of clinical compound diagnosis.

RESULTS: Eighty-nine non-HIV-infected patients were recruited, with dyspnea as the primary symptom (69.66%) and solid malignant tumor as the most common underlying disease (20.22%). Taking clinical compound diagnosis as the reference standard, the sensitivity, specificity, negative predictive value and positive predictive value of mNGS were higher than those detected by PCR and serum BDG. Among 42 non-HIV-infected patients with PJP who underwent mNGS and conventional pathogen detection of BALF, 6 had simple PJ infection and 36 had combined PJ infection. The detection rate of mNGS in mixed infections was significantly higher than that of conventional pathogen detection (85.71 vs 61.70%, P = 0.012). A total of 127 pathogens were detected in BALF using mNGS, among which fungi had the highest detection rate (46.46%). The fungi, viruses and bacteria detected were mainly Pneumocystis jirovecii, human gammaherpesvirus 4 and Acinetobacter baumannii.

CONCLUSION: mNGS is highly effective in diagnosing non-HIV-infected patients with PJP and exhibits ideal performance in the detection of co-pathogens. In addition, it has certain value for clinical diagnosis and guidance of targeted anti-infective drug treatment.},
}

@article {pmid38627869,
year = {2024},
author = {Ortiz Sanjuán, JM and Argüello, H and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Ekhlas, D and Burgess, CM and Manzanilla, EG},
title = {Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {18},
pmid = {38627869},
issn = {2524-4671},
support = {0376//Teagasc Walsh Scholarship Programme/ ; 0376//Teagasc Walsh Scholarship Programme/ ; BEAGAL-18-106//Spanish Government (Ministerio de Educación y Formación Profesional)/ ; },
abstract = {BACKGROUND: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period.

RESULTS: Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence.

CONCLUSION: Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.},
}

@article {pmid38627868,
year = {2024},
author = {Ho, M and Nguyen, HN and Van Hoang, M and Bui, TTT and Vu, BQ and Dinh, THT and Vo, HTM and Blaydon, DC and Eldirany, SA and Bunick, CG and Bui, CB},
title = {Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {38},
pmid = {38627868},
issn = {1479-7364},
support = {K08AR070290/AR/NIAMS NIH HHS/United States ; },
abstract = {BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI.

RESULTS: This case-control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing.

CONCLUSIONS: Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.},
}

@article {pmid38622339,
year = {2024},
author = {Salojärvi, J and Rambani, A and Yu, Z and Guyot, R and Strickler, S and Lepelley, M and Wang, C and Rajaraman, S and Rastas, P and Zheng, C and Muñoz, DS and Meidanis, J and Paschoal, AR and Bawin, Y and Krabbenhoft, TJ and Wang, ZQ and Fleck, SJ and Aussel, R and Bellanger, L and Charpagne, A and Fournier, C and Kassam, M and Lefebvre, G and Métairon, S and Moine, D and Rigoreau, M and Stolte, J and Hamon, P and Couturon, E and Tranchant-Dubreuil, C and Mukherjee, M and Lan, T and Engelhardt, J and Stadler, P and Correia De Lemos, SM and Suzuki, SI and Sumirat, U and Wai, CM and Dauchot, N and Orozco-Arias, S and Garavito, A and Kiwuka, C and Musoli, P and Nalukenge, A and Guichoux, E and Reinout, H and Smit, M and Carretero-Paulet, L and Filho, OG and Braghini, MT and Padilha, L and Sera, GH and Ruttink, T and Henry, R and Marraccini, P and Van de Peer, Y and Andrade, A and Domingues, D and Giuliano, G and Mueller, L and Pereira, LF and Plaisance, S and Poncet, V and Rombauts, S and Sankoff, D and Albert, VA and Crouzillat, D and de Kochko, A and Descombes, P},
title = {The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.},
journal = {Nature genetics},
volume = {56},
number = {4},
pages = {721-731},
pmid = {38622339},
issn = {1546-1718},
support = {1442190//NSF | Directorate for Biological Sciences (BIO)/ ; 2030871//NSF | Directorate for Biological Sciences (BIO)/ ; 343656//Academy of Finland (Suomen Akatemia)/ ; G056517N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BOF.MET.2021.0005.01//Universitair Ziekenhuis Gent (Ghent University Hospital)/ ; },
mesh = {*Coffea/genetics ; Coffee ; Genome, Plant/genetics ; Metagenomics ; Plant Breeding ; },
abstract = {Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.},
}

*Coffea/genetics
Coffee
Genome, Plant/genetics
Metagenomics
Plant Breeding

@article {pmid38489588,
year = {2024},
author = {David, G and Bertolotti, A and Layer, R and Scofield, D and Hayward, A and Baril, T and Burnett, HA and Gudmunds, E and Jensen, H and Husby, A},
title = {Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.},
journal = {Genome biology and evolution},
volume = {16},
number = {4},
pages = {},
pmid = {38489588},
issn = {1759-6653},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Genomics ; *Genome ; Metagenomics ; Polymorphism, Single Nucleotide ; },
abstract = {Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.},
}

*Genomics
*Genome
Metagenomics
Polymorphism, Single Nucleotide

@article {pmid38627797,
year = {2024},
author = {Lv, Y and Liu, X},
title = {Hemorrhagic cystitis induced by JC polyomavirus infection following COVID-19: a case report.},
journal = {BMC urology},
volume = {24},
number = {1},
pages = {87},
pmid = {38627797},
issn = {1471-2490},
abstract = {JC polyomavirus (JCPyV) is a human polyomavirus that can establish lifelong persistent infection in the majority of adults. It is typically asymptomatic in immunocompetent individuals. However, there is a risk of developing progressive multifocal leukoencephalopathy (PML) in immunocompromised or immunosuppressed patients. Though JCPyV commonly resides in the kidney-urinary tract, its involvement in urinary system diseases is extremely rare. Here, we reported a case of a 60-year-old male patient with coronavirus disease 2019 (COVID-19) infection who developed hemorrhagic cystitis after receiving treatment with nirmatrelvir 300 mg/ritonavir 100 mg quaque die (QD). Subsequent metagenomic next-generation sequencing (mNGS) confirmed the infection to be caused by JCPyV type 2. Then, human immunoglobulin (PH4) for intravenous injection at a dose of 25 g QD was administered to the patient. Three days later, the hematuria resolved. This case illustrates that in the setting of compromised host immune function, JCPyV is not limited to causing central nervous system diseases but can also exhibit pathogenicity in the urinary system. Moreover, mNGS technology facilitates rapid diagnosis of infectious etiology by clinical practitioners, contributing to precise treatment for patients.},
}

@article {pmid38627687,
year = {2024},
author = {Zhang, K and Paul, K and Jacobs, JP and Cockburn, MG and Bronstein, JM and Del Rosario, I and Ritz, B},
title = {Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study.},
journal = {Environmental health : a global access science source},
volume = {23},
number = {1},
pages = {41},
pmid = {38627687},
issn = {1476-069X},
support = {K01AG07204401/AG/NIA NIH HHS/United States ; R01ES031106/ES/NIEHS NIH HHS/United States ; },
abstract = {BACKGROUND: Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans.

METHODS: We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders.

RESULTS: OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6.

CONCLUSION: In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.},
}

@article {pmid38627615,
year = {2024},
author = {Peres da Silva, R and Suphavilai, C and Nagarajan, N},
title = {MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes.},
journal = {BMC bioinformatics},
volume = {25},
number = {Suppl 1},
pages = {153},
pmid = {38627615},
issn = {1471-2105},
abstract = {BACKGROUND: With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of higher sequencing error rates. While alignment-based methods are generally slower, k-mer-based taxonomic classifiers can overcome this limitation, potentially at the expense of lower sensitivity for strains and species that are not in the database.

RESULTS: We present MetageNN, a memory-efficient long-read taxonomic classifier that is robust to sequencing errors and missing genomes. MetageNN is a neural network model that uses short k-mer profiles of sequences to reduce the impact of distribution shifts on error-prone long reads. Benchmarking MetageNN against other machine learning approaches for taxonomic classification (GeNet) showed substantial improvements with long-read data (20% improvement in F1 score). By utilizing nanopore sequencing data, MetageNN exhibits improved sensitivity in situations where the reference database is incomplete. It surpasses the alignment-based MetaMaps and MEGAN-LR, as well as the k-mer-based Kraken2 tools, with improvements of 100%, 36%, and 23% respectively at the read-level analysis. Notably, at the community level, MetageNN consistently demonstrated higher sensitivities than the previously mentioned tools. Furthermore, MetageNN requires < 1/4th of the database storage used by Kraken2, MEGAN-LR and MMseqs2 and is > 7× faster than MetaMaps and GeNet and > 2× faster than MEGAN-LR and MMseqs2.

CONCLUSION: This proof of concept work demonstrates the utility of machine-learning-based methods for taxonomic classification using long reads. MetageNN can be used on sequences not classified by conventional methods and offers an alternative approach for memory-efficient classifiers that can be optimized further.},
}

@article {pmid38627038,
year = {2024},
author = {Girão, M and Alexandrino, DAM and Cao, W and Costa, I and Jia, Z and Carvalho, MF},
title = {Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16620},
doi = {10.1111/1462-2920.16620},
pmid = {38627038},
issn = {1462-2920},
support = {SFRH/BD/145646/2019//Fundação para a Ciência e a Tecnologia/ ; UIDB/04423/2020//European Regional Development Fund/ ; UIDP/04423/2020//European Regional Development Fund/ ; CEECIND/02968/2017//Fundação para a Ciência e Tecnologia/ ; //Fundo Social Europeu and Programa Operacional Potencial Humano/ ; C644915664-00000026//WP9 - Portuguese Blue Biobank under the Blue Economy Pact/ ; },
abstract = {Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.},
}

@article {pmid38627246,
year = {2024},
author = {Siqueira, JAM and Teixeira, DM and da Piedade, GJL and de Oliveira Souza, C and Moura, TCF and de Nazaré Miranda Bahia, M and Brasiliense, DM and de Sousa Santos, DSA and de Sa Morais, LLC and de Fátima Lobato da Silva, D and Carneiro, BS and da Costa Pinheiro, K and Sousa Junior, EC and Catete, CP and de Paula Souza E Guimarães, RJ and Ferreira, JL and Dias das Chagas Junior, W and Machado, RS and Tavares, FN and Resque, HR and Dos Santos Lobo, P and de Fátima Dos Santos Guerra, S and Soares, LS and da Silva, LD and Gabbay, YB},
title = {Environmental Health of Water Bodies From a Brazilian Amazon Metropolis Based On a Conventional and Metagenomic Approach.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae101},
pmid = {38627246},
issn = {1365-2672},
abstract = {AIMS: The present study aimed to use a conventional and metagenomic approach to investigate the microbiological diversity of water bodies in a network of drainage channels and rivers located in the central area of the city of Belém, Northern Brazil, which is considered one of the largest cities in the Brazilian Amazon.

METHODS AND RESULTS: In eight of the analyzed points, both bacterial and viral microbiological indicators of environmental contamination, the physical-chemical and metals were assessed. The bacterial resistance genes, drug resistance mechanisms, and viral viability in the environment were also assessed. A total of 473 families of bacteria and 83 families of viruses were identified. Based on the analysis of metals, the levels of three metals (Cd, Fe, and Mn) were found to be above the recommended acceptable level by local legislation. The levels of the following three physicochemical parameters were also higher than recommended: Biochemical Oxygen Demand, dissolved oxygen, and turbidity. Sixty-three bacterial resistance genes that conferred resistance to 13 different classes of antimicrobials were identified. Further, five mechanisms of antimicrobial resistance were identified and viral viability in the environment was confirmed.

CONCLUSIONS: Intense human actions combined with a lack of public policies and poor environmental education of the population cause environmental degradation, especially in water bodies. Thus, urgent interventions are warranted to restore the quality of this precious and scarce asset worldwide.},
}

@article {pmid38626494,
year = {2024},
author = {Zhu, Y and Ke, M and Yu, Z and Lei, C and Liu, M and Yang, Y and Lu, T and Zhou, NY and Peijnenburg, WJGM and Tang, T and Qian, H},
title = {Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana.},
journal = {Environment international},
volume = {186},
number = {},
pages = {108655},
doi = {10.1016/j.envint.2024.108655},
pmid = {38626494},
issn = {1873-6750},
abstract = {The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.},
}

@article {pmid38626487,
year = {2024},
author = {Zhou, Z and Shi, X and Bhople, P and Jiang, J and Chater, CCC and Yang, S and Perez-Moreno, J and Yu, F and Liu, D},
title = {Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120895},
doi = {10.1016/j.jenvman.2024.120895},
pmid = {38626487},
issn = {1095-8630},
abstract = {Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4[+]-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.},
}

@article {pmid38626484,
year = {2024},
author = {Su, X and Zhang, L and Meng, H and Wang, H and Zhao, J and Sun, X and Song, X and Zhang, X and Mao, L},
title = {Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO2 fixation pathways in coastal saline soil.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120743},
doi = {10.1016/j.jenvman.2024.120743},
pmid = {38626484},
issn = {1095-8630},
abstract = {Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.},
}

@article {pmid38626236,
year = {2024},
author = {Remenyik, J and Csige, L and Dávid, P and Fauszt, P and Szilágyi-Rácz, AA and Szőllősi, E and Bacsó, ZR and Szepsy Jnr, I and Molnár, K and Rácz, C and Fidler, G and Kállai, Z and Stündl, L and Dobos, AC and Paholcsek, M},
title = {Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300563},
doi = {10.1371/journal.pone.0300563},
pmid = {38626236},
issn = {1932-6203},
abstract = {A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.},
}

@article {pmid38625103,
year = {2024},
author = {Zhao, Z and Li, C and Huang, J and Yuan, X and Cui, Y and Liu, Y and Zhou, Y and Zhu, Z and Zhang, Z},
title = {Phlorizin Limits Bovine Viral Diarrhea Virus Infection in Mice via Regulating Gut Microbiota Composition.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c01228},
pmid = {38625103},
issn = {1520-5118},
abstract = {Phlorizin (PHZ) is one of the main pharmacologically active ingredients in Lithocarpus polystachyus. We have previously shown that PHZ inhibits the replication of bovine viral diarrhea virus (BVDV), but the exact antiviral mechanism, especially in vivo, is still unknown. Here, we further confirm that PHZ has good protective effects in BVDV-infected mice. We analyzed BVDV-induced CD3[+], CD4[+], and CD8[+] T cells among peripheral blood lymphocytes and found that PHZ significantly restored their percentage. Metagenomic analyses revealed that PHZ markedly improved the richness and diversity of intestinal microbiota and increased the abundance of potentially health-related microbes (families Lachnosipiraceae, Ruminococcaceae, and Oscillospiraceae). Specifically, the relative abundance of short chain fatty acid (SCFA)-producing bacteria, including Lachnospiraceae_UCG-006, unclassified_f_Ruminococcaceae, Oscillibacter, Intestinimonas, Blautia, and Lachnoclostridium increased significantly after PHZ treatment. Interestingly, BVDV-infected mice that received fecal microbiota from PHZ-treated mice (PHZ-FMT) had a significantly lower viral load in the duodenum and jejunum than untreated mice. Pathological lesions of duodenum and jejunum were also greatly reduced in the PHZ-FMT group, confirming a significant antiviral effect. These findings show that gut microbiota play an important role in PHZ's antiviral activity and suggest that their targeted intervention might be a promising endogenous strategy to prevent and control BVDV.},
}

@article {pmid38625060,
year = {2024},
author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC},
title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae062},
pmid = {38625060},
issn = {1751-7370},
abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing the spatial reach of their impact on trace gas-oxidizing microbes in the surrounding soils. This study assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA quantities and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest that this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy and/or carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests that the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.},
}

@article {pmid38625036,
year = {2024},
author = {Srikrishna, D},
title = {Pentagon Found Daily, Metagenomic Detection of Novel Bioaerosol Threats to Be Cost-Prohibitive: Can Virtualization and AI Make It Cost-Effective?.},
journal = {Health security},
volume = {22},
number = {2},
pages = {108-129},
doi = {10.1089/hs.2023.0048},
pmid = {38625036},
issn = {2326-5108},
abstract = {In 2022, the Pentagon Force Protection Agency found threat agnostic detection of novel bioaerosol threats to be "not feasible for daily operations" due to the cost of reagents used for metagenomics, cost of sequencing instruments, and cost of labor for subject matter experts to analyze bioinformatics. Similar operational difficulties might extend to many of the 280,000 buildings (totaling 2.3 billion square feet) at 5,000 secure US Department of Defense military sites, 250 Navy ships, as well as many civilian buildings. These economic barriers can still be addressed in a threat agnostic manner by dynamically pooling samples from dry filter units, called spike-triggered virtualization, whereby pooling and sequencing depth are automatically modulated based on novel biothreats in the sequencing output. By running at a high average pooling factor, the daily and annual cost per dry filter unit can be reduced by 10 to 100 times depending on the chosen trigger thresholds. Artificial intelligence can further enhance the sensitivity of spike-triggered virtualization. The risk of infection during the 12- to 24-hour window between a bioaerosol incident and its detection remains, but in some cases it can be reduced by 80% or more with high-speed indoor air cleaning exceeding 12 air changes per hour, which is similar to the rate of air cleaning in passenger airplanes in flight. That level of air changes per hour or higher is likely to be cost-prohibitive using central heating ventilation and air conditioning systems, but it can be achieved economically by using portable air filtration in rooms with typical ceiling heights (less than 10 feet) for a cost of approximately $0.50 to $1 per square foot for do-it-yourself units and $2 to $5 per square foot for high-efficiency particulate air filters.},
}

@article {pmid38624235,
year = {2024},
author = {Osborn, LJ and Fissel, J and Gomez, S and Mestas, J and Flores-Vazquez, J and Lee, J and Hakimjavadi, H and Costales, C and Dien Bard, J},
title = {Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0174923},
doi = {10.1128/jcm.01749-23},
pmid = {38624235},
issn = {1098-660X},
abstract = {UNLABELLED: The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively.

IMPORTANCE: To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.},
}

@article {pmid38624222,
year = {2024},
author = {Ali, R and Chaluvadi, SR and Wang, X and Hazzouri, KM and Sudalaimuthuasari, N and Rafi, M and Al-Nuaimi, M and Sasi, S and Antepenko, E and Bennetzen, JL and Amiri, KMA},
title = {Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0361723},
doi = {10.1128/spectrum.03617-23},
pmid = {38624222},
issn = {2165-0497},
abstract = {We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.},
}

@article {pmid38623900,
year = {2024},
author = {Zhang, Y and Lo, KL and Liman, AN and Feng, XP and Ye, W},
title = {Tongue-Coating Microbial and Metabolic Characteristics in Halitosis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241230067},
doi = {10.1177/00220345241230067},
pmid = {38623900},
issn = {1544-0591},
abstract = {Halitosis is a common oral condition, which leads to social embarrassment and affects quality of life. Cumulative evidence has suggested the association of tongue-coating microbiome with the development of intraoral halitosis. The dynamic variations of tongue-coating microbiota and metabolites in halitosis have not been fully elucidated. Therefore, the present study aimed to determine the tongue-coating microbial and metabolic characteristics in halitosis subjects without other oral diseases using metagenomics and metabolomics analysis. The participants underwent oral examination, halitosis assessment, and tongue-coating sample collection for the microbiome and metabolome analysis. It was found that the microbiota richness and diversity were significantly elevated in the halitosis group. Furthermore, species from Actinomyces, Prevotella, Veillonella, and Solobacterium were significantly more abundant in the halitosis group. However, the Rothia and Streptococcus species exhibited opposite tendencies. Eleven Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in the halitosis tongue coatings, including cysteine and methionine metabolism. Functional genes related to sulfur, indole, skatole, and cadaverine metabolic processes (such as serA, metH, metK and dsrAB) were identified to be more abundant in the halitosis samples. The metabolome analysis revealed that indole-3-acetic, ornithine, and L-tryptophan were significantly elevated in the halitosis samples. Furthermore, it was observed that the values of volatile sulfur compounds and indole-3-acetic abundances were positively correlated. The multiomics analysis identified the metagenomic and metabolomic characteristics to differentiate halitosis from healthy individuals using the least absolute shrinkage and selection operator logistic regression and random forest classifier. A total of 19 species and 39 metabolites were identified as features in halitosis patients, which included indole-3-acetic acid, Bacillus altitudinis, Candidatus Saccharibacteria, and Actinomyces species. In conclusion, an evident shift in microbiome and metabolome characteristics was observed in the halitosis tongue coating, which may have a potential etiological significance and provide novel insights into the mechanism for halitosis.},
}

@article {pmid38623014,
year = {2024},
author = {Wang, Q and Yang, JH and Chen, X and Zhang, YJ and Zhu, XY and Li, XF and Su, J and Sa, CRG and Yang, B and Lu, GP and Xu, Y},
title = {[Metagenomic next-generation sequencing-based retrospective investigation of the drug resistance sites of mycoplasma pneumoniae in children].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {62},
number = {5},
pages = {457-461},
doi = {10.3760/cma.j.cn112140-20240105-00019},
pmid = {38623014},
issn = {0578-1310},
support = {2021YFC2701800, 2021YFC2701801//National Strategic Plan for Research and Development/ ; },
abstract = {Objective: To analyze the drug-resistant gene loci of Mycoplasma pneumoniae (MP) using metagenomic next-generation sequencing (mNGS). Methods: From November 2022 to October 2023, 697 clinical samples (including sputum, alveolar lavage fluid and blood) of 686 children with Mycoplasma pneumoniae positive detected by mNGS were retrospectively analyzed. Samples were divided into intensive care unit (ICU) group and non-ICU group, Chi-square test was used to compare groups, and Mann-Kendall trend test was used to analyze the change trend of the detection rate of drug resistance gene loci over time. Results: Of the 697 samples, 164 were from the ICU group and 533 were from the non-ICU group. The detection rate of Mycoplasma pneumoniae resistance gene was 44.3% (309/697), and all detected drug-resistant gene loci of MP were A2063G. The detection rate of Mycoplasma pneumoniae in ICU group was 50.0% (82/164), and the detection rates of Mycoplasma pneumoniae resistance gene loci in sputum, alveolus lavage fluid and blood samples were 75.0% (18/24) and 48.4% (62/128), respectively. The detection rate in sputum was higher than alveolus lavage fluid samples (χ[2]=5.72,P=0.017). The detection rate of Mycoplasma pneumoniae in non-ICU group was 42.6% (227/533), the detection rate of Mycoplasma pneumoniae resistance gene loci in sputum and alveolar lavage fluid was 40.0% (16/40), 44.3% (201/454), and no detection rate in blood samples (0/12). There was no significant difference in the detection rate of alveolar lavage fluid and sputum (χ[2]=0.27, P=0.602). From November 2022 to October 2023, the detection rate of submitted samples showed an increasing trend month by month (overall: Z=3.99, ICU inspection group: Z=2.93, non-ICU group: Z=3.01, all P<0.01). Among the bacteria commonly detected with Mycoplasma pneumoniae, Streptococcus pneumoniae accounted for the highest proportion, the detection rate was 15.5% (108/697), and Epstein-Barr virus accounted for the highest proportion of 17.6% (123/697). Conclusions: From November 2022 to October 2023, the detection rate of Mycoplasma pneumoniae drug resistance gene loci showed an increasing trend. The detection rate of drug resistance gene loci in sputum samples of ICU group was higher than alveolus lavage fluid. No new drug resistance site were detected.},
}

@article {pmid38622738,
year = {2024},
author = {Wu, LY and Wijesekara, Y and Piedade, GJ and Pappas, N and Brussaard, CPD and Dutilh, BE},
title = {Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {97},
pmid = {38622738},
issn = {1474-760X},
support = {Consolidator grant 865694//H2020 European Research Council/ ; Consolidator grant 865694//H2020 European Research Council/ ; 955974//H2020 Marie Skłodowska-Curie Actions/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS: We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS: Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.},
}

@article {pmid38622723,
year = {2024},
author = {Gan, M and Zhang, Y and Yan, G and Wang, Y and Lu, G and Wu, B and Chen, W and Zhou, W},
title = {Antimicrobial resistance prediction by clinical metagenomics in pediatric severe pneumonia patients.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {33},
pmid = {38622723},
issn = {1476-0711},
support = {2021YFC2701800 and 2021YFC2701805//National Key Research and Development Program of China/ ; 2022YFC2703603//National Key Research and Development Program of China/ ; 22Y11902700//the Science and Technology Commission of Shanghai Municipality/ ; MTP2022A014//the China Primary Health Care Foundation/ ; 2023ZDFC0103//the Shanghai Municipal Health System key supports discipline projects/ ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major threat to children's health, particularly in respiratory infections. Accurate identification of pathogens and AMR is crucial for targeted antibiotic treatment. Metagenomic next-generation sequencing (mNGS) shows promise in directly detecting microorganisms and resistance genes in clinical samples. However, the accuracy of AMR prediction through mNGS testing needs further investigation for practical clinical decision-making.

METHODS: We aimed to evaluate the performance of mNGS in predicting AMR for severe pneumonia in pediatric patients. We conducted a retrospective analysis at a tertiary hospital from May 2022 to May 2023. Simultaneous mNGS and culture were performed on bronchoalveolar lavage fluid samples obtained from pediatric patients with severe pneumonia. By comparing the results of mNGS detection of microorganisms and antibiotic resistance genes with those of culture, sensitivity, specificity, positive predictive value, and negative predictive value were calculated.

RESULTS: mNGS detected bacterial in 71.7% cases (86/120), significantly higher than culture (58/120, 48.3%). Compared to culture, mNGS demonstrated a sensitivity of 96.6% and a specificity of 51.6% in detecting pathogenic microorganisms. Phenotypic susceptibility testing (PST) of 19 antibiotics revealed significant variations in antibiotics resistance rates among different bacteria. Sensitivity prediction of mNGS for carbapenem resistance was higher than penicillins and cephalosporin (67.74% vs. 28.57%, 46.15%), while specificity showed no significant difference (85.71%, 75.00%, 75.00%). mNGS also showed a high sensitivity of 94.74% in predicting carbapenem resistance in Acinetobacter baumannii.

CONCLUSIONS: mNGS exhibits variable predictive performance among different pathogens and antibiotics, indicating its potential as a supplementary tool to conventional PST. However, mNGS currently cannot replace conventional PST.},
}

@article {pmid38622589,
year = {2024},
author = {Gao, J and Yang, Y and Xiang, X and Zheng, H and Yi, X and Wang, F and Liang, Z and Chen, D and Shi, W and Wang, L and Wu, D and Feng, S and Huang, Q and Li, X and Shu, W and Chen, R and Zhong, N and Wang, Z},
title = {Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {165},
pmid = {38622589},
issn = {1465-993X},
abstract = {Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10[-5]), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10[-8]). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.},
}

@article {pmid38622147,
year = {2024},
author = {Yu, M and Zhang, M and Zeng, R and Cheng, R and Zhang, R and Hou, Y and Kuang, F and Feng, X and Dong, X and Li, Y and Shao, Z and Jin, M},
title = {Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3228},
pmid = {38622147},
issn = {2041-1723},
support = {41976084//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.},
}

@article {pmid38621967,
year = {2024},
author = {Wang, ZH and Liu, S and Yang, G and Lu, ZY and Zhu, RQ and Li, Y and Shen, Y and Kang, LP and Chen, ML},
title = {[Effects of organic fertilizer from traditional Chinese medicine residues on growth and soil microbial community of Salvia miltiorrhiza by metagenomic technique].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {5},
pages = {1206-1216},
doi = {10.19540/j.cnki.cjcmm.20231213.101},
pmid = {38621967},
issn = {1001-5302},
abstract = {Soil microbiome is a key evaluation index of soil health. Previous studies have shown that organic fertilizer from traditional Chinese medicine(TCM)residues can improve the yield and quality of cultivated traditional Chinese medicinal materials. However, there are few reports on the effects of organic fertilizer from TCM residues on soil microbiome. Therefore, on the basis of evaluating the effects of organic fertilizer from TCM residues on the yield and quality of cultivated Salvia miltiorrhiza, the metagenomic sequencing technique was used to study the effects of organic fertilizer from TCM residues on rhizosphere microbiome community and function of cultivated S. miltiorrhiza. The results showed that:(1) the application of organic fertilizer from TCM residues promoted the growth of S. miltiorrhiza and the accumulation of active components, and the above-ground and underground dry weight and fresh weight of S. miltiorrhiza increased by 371.4%, 288.3%, 313.4%, and 151.9%. The increases of rosmarinic acid and salvianolic acid B were 887.0% and 183.0%.(2)The application of organic fertilizer from TCM residues significantly changed the rhizosphere bacterial and fungal community structures, and the microbial community composition was significantly different.(3)The relative abundance of soil-beneficial bacteria, such as Nitrosospira multiformis, Bacillus subtilis, Lysobacter enzymogenes, and Trichoderma was significantly increased by the application of organic fertilizer from TCM residues.(4)KEGG function prediction analysis showed that metabolism-related microorganisms were more easily enriched in the soil environment after organic fertilizer application. The abundance of functional genes related to nitrification and denitrification could also be increased after the application of organic fertilizer from TCM residues. The results of this study provide guidance for the future application of organic fertilizer from TCM residues in the cultivation of traditio-nal Chinese medicinal materials and enrich the content of green cultivation technology of traditional Chinese medicinal materials.},
}

@article {pmid38621394,
year = {2024},
author = {Paull, JS and Petros, BA and Brock-Fisher, TM and Jalbert, SA and Selser, VM and Messer, KS and Dobbins, ST and DeRuff, KC and Deng, D and Springer, M and Sabeti, PC},
title = {Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(23)00399-3},
pmid = {38621394},
issn = {2666-5247},
abstract = {BACKGROUND: Sequencing of SARS-CoV-2 from rapid diagnostic tests (RDTs) can bolster viral genomic surveillance efforts; however, approaches to maximise and standardise pathogen genome recovery from RDTs remain underdeveloped. We aimed to systematically optimise the elution of genetic material from RDT components and to evaluate the efficacy of RDT sequencing for outbreak investigation.

METHODS: In this laboratory and cohort-based study we seeded RDTs with inactivated SARS-CoV-2 to optimise the elution of genomic material from RDT lateral flow strips. We measured the effect of changes in buffer type, time in buffer, and rotation on PCR cycle threshold (Ct) value. We recruited individuals older than 18 years residing in the greater Boston area, MA, USA, from July 18 to Nov 5, 2022, via email advertising to students and staff at Harvard University, MA, USA, and via broad social media advertising. All individuals recruited were within 5 days of a positive diagnostic test for SARS-CoV-2; no other relevant exclusion criteria were applied. Each individual completed two RDTs and one PCR swab. On Dec 29, 2022, we also collected RDTs from a convenience sample of individuals who were positive for SARS-CoV-2 and associated with an outbreak at a senior housing facility in MA, USA. We extracted all returned PCR swabs and RDT components (ie, swab, strip, or buffer); samples with a Ct of less than 40 were subject to amplicon sequencing. We compared the efficacy of elution and sequencing across RDT brands and components and used RDT-derived sequences to infer transmission links within the outbreak at the senior housing facility. We conducted metagenomic sequencing of negative RDTs from symptomatic individuals living in the senior housing facility.

FINDINGS: Neither elution duration of greater than 10 min nor rotation during elution impacted viral titres. Elution in Buffer AVL (Ct=31·4) and Tris-EDTA Buffer (Ct=30·8) were equivalent (p=0·34); AVL outperformed elution in lysis buffer and 50% lysis buffer (Ct=40·0, p=0·0029 for both) as well as Universal Viral Transport Medium (Ct=36·7, p=0·079). Performance of RDT strips was poorer than that of matched PCR swabs (mean Ct difference 10·2 [SD 4·3], p<0·0001); however, RDT swabs performed similarly to PCR swabs (mean Ct difference 4·1 [5·2], p=0·055). No RDT brand significantly outperformed another. Across sample types, viral load predicted the viral genome assembly length. We assembled greater than 80% complete genomes from 12 of 17 RDT-derived swabs, three of 18 strips, and four of 11 residual buffers. We generated outbreak-associated SARS-CoV-2 genomes using both amplicon and metagenomic sequencing and identified multiple introductions of the virus that resulted in downstream transmission.

INTERPRETATION: RDT-derived swabs are a reasonable alternative to PCR swabs for viral genomic surveillance and outbreak investigation. RDT-derived lateral flow strips yield accurate, but significantly fewer, viral reads than matched PCR swabs. Metagenomic sequencing of negative RDTs can identify viruses that might underlie patient symptoms.

FUNDING: The National Science Foundation, the Hertz Foundation, the National Institute of General Medical Sciences, Harvard Medical School, the Howard Hughes Medical Institute, the US Centers for Disease Control and Prevention, the Broad Institute and the National Institute of Allergy and Infectious Diseases.},
}

@article {pmid38621316,
year = {2024},
author = {Wang, S and Nie, W and Gu, Q and Wang, X and Yang, D and Li, H and Wang, P and Liao, W and Huang, J and Yuan, Q and Zhou, S and Ahmad, I and Kotaro, K and Chen, G and Zhu, B},
title = {Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database.},
journal = {Water research},
volume = {256},
number = {},
pages = {121572},
doi = {10.1016/j.watres.2024.121572},
pmid = {38621316},
issn = {1879-2448},
abstract = {The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.},
}

@article {pmid38620144,
year = {2024},
author = {Eme, L and Tamarit, D},
title = {Microbial Diversity and Open Questions about the Deep Tree of Life.},
journal = {Genome biology and evolution},
volume = {16},
number = {4},
pages = {},
doi = {10.1093/gbe/evae053},
pmid = {38620144},
issn = {1759-6653},
support = {803151/ERC_/European Research Council/International ; },
abstract = {In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.},
}

@article {pmid38619550,
year = {2024},
author = {Wang, X and Guo, H and Wang, J and He, P and Kuzyakov, Y and Ma, M and Ling, N},
title = {Microbial phosphorus-cycling genes in soil under global change.},
journal = {Global change biology},
volume = {30},
number = {4},
pages = {e17281},
doi = {10.1111/gcb.17281},
pmid = {38619550},
issn = {1365-2486},
support = {lzujbky-2022-ct04//Fundamental Research Funds for the Central Universities/ ; 42277100//National Natural Science Foundation of China/ ; },
abstract = {The ongoing climate change on the Tibetan Plateau, leading to warming and precipitation anomalies, modifies phosphorus (P) cycling in alpine meadow soils. However, the interactions and cascading effects of warming and precipitation changes on the key "extracellular" and "intracellular" P cycling genes (PCGs) of bacteria are largely unknown for these P-limited ecosystems. We used metagenomics to analyze the individual and combined effects of warming and altered precipitation on soil PCGs and P transformation in a manipulation experiment. Warming and increased precipitation raised Olsen-P (bioavailable P, AP) by 13% and 20%, respectively, mainly caused by augmented hydrolysis of organic P compounds (NaOH-Po). The decreased precipitation reduced soil AP by 5.3%. The richness and abundance of the PCGs' community in soils on the cold Tibetan plateau were more sensitive to warming than altered precipitation. The abundance of PCGs and P cycling processes decreased under the influence of individual climate change factors (i.e., warming and altered precipitation alone), except for the warming combined with increased precipitation. Pyruvate metabolism, phosphotransferase system, oxidative phosphorylation, and purine metabolism (all "intracellular" PCG) were closely correlated with P pools under climate change conditions. Specifically, warming recruited bacteria with the phoD and phoX genes, which encode enzymes responsible for phosphoester hydrolysis (extracellular P cycling), strongly accelerated organic P mineralization and so, directly impacted P bioavailability in alpine soil. The interactions between warming and altered precipitation profoundly influenced the PCGs' community and facilitated microbial adaptation to these environmental changes. Warming combined with increased precipitation compensated for the detrimental impacts of the individual climate change factors on PCGs. In conclusion, warming combined with rising precipitation has boosting effect on most P-related functions, leading to the acceleration of P cycling within microbial cells and extracellularly, including mineralization and more available P release for microorganisms and plants in alpine soils.},
}

@article {pmid38618705,
year = {2024},
author = {Sarkar, S and Anyaso-Samuel, S and Qiu, P and Datta, S},
title = {Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors.},
journal = {Statistics in medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/sim.10058},
pmid = {38618705},
issn = {1097-0258},
abstract = {Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.},
}

@article {pmid38618581,
year = {2024},
author = {Cheng, X and Li, T and Wu, F and Liu, D},
title = {Clinical Manifestation, mNGS Based Diagnosis and Treatment of Pulmonary Mucormycosis with Rhizopus delemar in a Diabetic Patient.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1379-1384},
pmid = {38618581},
issn = {1178-6973},
abstract = {Pulmonary mucormycosis is a severe and often fatal disease that commonly affects patients with underlying conditions, such as diabetes. Early diagnosis and appropriate treatment are crucial for improving survival rates. However, clinical diagnosis remains challenging due to difficulty in obtaining etiological evidence. In this particular case, the patient presented with a cough-producing bloody sputum, and a chest CT revealed lesions in the right upper lobe of the lung. The patient was ultimately diagnosed with pulmonary mucormycosis caused by Rhizopus delemar through clinical bronchoscopy biopsy and metagenomic next-generation sequencing (mNGS) analysis of bronchoalveolar lavage fluid sample. Subsequently, antifungal therapy using the less toxic Amphotericin B cholesterol Organosulfate complex was initiated, improving the patient's condition. In conclusion, our findings underscore the potential of mNGS to provide an accurate and rapid etiological diagnosis of pulmonary mucormycosis, offering a foundation for treatment.},
}

@article {pmid38617453,
year = {2024},
author = {Chen, SJ and Zhang, DY and Wu, X and Zhang, FM and Cui, BT and Huang, YH and Zhang, ZL and Wang, R and Bai, FH},
title = {Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.},
journal = {World journal of gastroenterology},
volume = {30},
number = {11},
pages = {1572-1587},
pmid = {38617453},
issn = {2219-2840},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported.

AIM: To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.

METHODS: We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure.

RESULTS: Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT.

CONCLUSION: WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.},
}

@article {pmid38617439,
year = {2024},
author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K},
title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2339158},
pmid = {38617439},
issn = {2000-2297},
abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.

METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).

RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of α-diversity (p < 0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in β-diversity between H. pylori-positive and negative child specimens (p < 0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p < 0.01 and p < 0.05, respectively).

CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.},
}

@article {pmid38617292,
year = {2024},
author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Vanhoy Walsh, M and Meyerhoffer, AK and Vintila, S and Maier, J and Richie, T and Theriot, CM and Kleiner, M},
title = {Dietary protein source strongly alters gut microbiota composition and function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.04.588169},
pmid = {38617292},
abstract = {The source of protein in a persons diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices have major impacts on the composition and function of the intestinal microbiota that ultimately mediate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determine the effects of seven different sources of dietary protein on the gut microbiota in mice. We apply an integrated metagenomics-metaproteomics approach to simultaneously investigate the effects of these dietary protein sources on the gut microbiotas composition and function. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the phenotype of microbiota members on the molecular level because measured proteins allow us to infer the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial amino acid degrading proteins and proteins involved in the degradation of glycosylations on dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes and egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein source can change the gut microbiotas metabolism, which could have major implications in the context of gut microbiota mediated diseases.},
}

@article {pmid38616262,
year = {2024},
author = {Yao, Y and Xu, Q and Liang, W and Ji, S and Kosari, M and Xu, S and Zhu, Z and Mao, Z},
title = {Multi-organ involvement caused by Scedosporium apiospermum infection after near drowning: a case report and literature review.},
journal = {BMC neurology},
volume = {24},
number = {1},
pages = {124},
pmid = {38616262},
issn = {1471-2377},
support = {82171465//National Natural Science Fundation of China/ ; 81901303//National Natural Science Fundation of China/ ; },
abstract = {BACKGROUND: Scedosporium apiospermum (S. apiospermum) is a rare fungal pathogen that causes disseminated infections. It rarely affects immunocompetent individuals and has a poor prognosis.

CASE PRESENTATION: A 37-year-old woman presented with multiple lesions in the lungs, brain, and eyes, shortly after near drowning in a car accident. The primary symptoms were chest tightness, limb weakness, headache, and poor vision in the left eye. S. apiospermum infection was confirmed by metagenomic next-generation sequencing (mNGS) of intracranial abscess drainage fluid, although intracranial metastases were initially considered. After systemic treatment with voriconazole, her symptoms improved significantly; however, she lost vision in her left eye due to delayed diagnosis.

CONCLUSION: While S. apiospermum infection is rare, it should be considered even in immunocompetent patients. Prompt diagnosis and treatment are essential. Voriconazole may be an effective treatment option.},
}

@article {pmid38615602,
year = {2024},
author = {Huang, P and Chen, Y and Li, Z and Zhang, B and Yu, S and Zhou, Y},
title = {Ammonia-dependent reducing power redistribution for purple phototrophic bacteria culture-based biohydrogen production.},
journal = {Water research},
volume = {256},
number = {},
pages = {121599},
doi = {10.1016/j.watres.2024.121599},
pmid = {38615602},
issn = {1879-2448},
abstract = {The global energy crisis has intensified the search for sustainable and clean alternatives, with biohydrogen emerging as a promising solution to address environmental challenges. Leveraging photo fermentation (PF) process, purple phototrophic bacteria (PPB) can harness reducing power derived from organic substrates to facilitate hydrogen production. However, existing studies report much lower H2 yields than theoretical value when using acetate as carbon source and ammonia as nitrogen source, primarily attributed to the widely employed pulse-feeding mode which suffers from ammonia inhibition effect on nitrogenase. To address this issue, a continuous feeding mode was applied to avoid ammonia accumulation in this study. On the other hand, other pathways like carbon fixation and polyhydroxyalkanoate (PHA) formation could compete reducing power with H2 production. However, the reducing power allocation under continuous feeding mode is not yet clear. In this study, the reducing power allocation and hydrogen production performance were evaluated under various ammonia loading, using acetate as carbon source and infrared LED at around 50 W·m[-2] as light source. The results show that (a) The absence of ammonia resulted in the best performance for hydrogen production, with 44 % of the reducing power distributed to H2 and the highest H2 volumetric productivity, while the allocation of reducing power to hydrogen production stopped when ammonia loading was above 7.6 mg NH4-N·L[-1]·d[-1]; (b) when PPB required to eliminate reducing power under ammonia limited conditions, PHA production was the preferred pathway followed by the hydrogen production pathway, but once PHA accumulation reached saturation, hydrogen generation pathway dominated; (c) under ammonia limited conditions, the TCA cycle was more activated rendering higher NADH (i.e. reducing power) production compared with that under ammonia sufficient conditions which was verified by metagenomics analysis, and all the hydrogen production, PHA accumulation and carbon fixation pathways were highly active to dissipate reducing power. This work provides the insight of reducing power distribution and PPB biohydrogen production variated by ammonia loading under continuous feeding mode.},
}

@article {pmid38585881,
year = {2024},
author = {Knuth, MM and Campos, CV and Smith, K and Hutchins, EK and Lewis, S and York, M and Coghill, LM and Franklin, C and MacFarlane, A and Ericsson, AC and Magnuson, T and Ideraabdullah, F},
title = {Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38585881},
support = {R21 DK122242/DK/NIDDK NIH HHS/United States ; R25 GM089569/GM/NIGMS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; T32 CA217824/CA/NCI NIH HHS/United States ; U42 OD010924/OD/NIH HHS/United States ; },
abstract = {Standard chow diet contributes to reproducibility in animal model experiments since chows differ in nutrient composition, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here, we measured the impact of diet (5V5M, 5V0G, 2920X, and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE), and developmental exposure (DE)) on growth & development, metabolic health indicators, and gut bacterial microbiota profiles across genetically identical C57BL6/J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on measured outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight, and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. Diet-induced beta diversity profiles were sex-dependent for LE mice. Compared to AE, LE drove 9X more diet-driven differentially abundant genera, majority of which were the result of inverse effects of 2920X and 5058. Our findings demonstrate that lifetime exposure to different chow diets has the greatest impact on reproducibility of experimental measures that are common components of preclinical mouse model studies. Importantly, weaning DE mice onto a uniform diet is likely an effective way to reduce unwanted phenotypic variability among experimental models.},
}

@article {pmid38615598,
year = {2024},
author = {Li, W and Wang, S and Zheng, D},
title = {Metagenomic next-generation sequencing for diagnosing severe leptospirosis in a patient suspected COVID-19: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {109},
number = {3},
pages = {116288},
doi = {10.1016/j.diagmicrobio.2024.116288},
pmid = {38615598},
issn = {1879-0070},
abstract = {Leptospirosis is a zoonotic and neglected waterborne disease caused by the pathogenic helical spirochetes. Early diagnosis of leptospirosis remains challenging due to non-specific symptoms and the limited availability of rapid point-of-care diagnostic tests. Herein, we present a case where a patient suspected of having COVID-19 was diagnosed with leptospirosis using metagenomic next-generation sequencing (mNGS). This case highlights the potential of mNGS to diagnose leptospirosis in the context of the COVID-19 pandemic.},
}

@article {pmid38614455,
year = {2024},
author = {Li, X and Kurahara, LH and Zhao, Z and Zhao, F and Ishikawa, R and Ohmichi, K and Li, G and Yamashita, T and Hashimoto, T and Hirano, M and Sun, Z and Hirano, K},
title = {The therapeutic effect of proteinase-activated receptor-1 antagonist on colitis-associated carcinogenesis.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcmgh.2024.04.001},
pmid = {38614455},
issn = {2352-345X},
abstract = {BACKGROUND & AIMS: Inflammatory bowel disease is associated with carcinogenesis, which limits the prognosis of the patients. The local expression of proteinases and proteinase-activated receptor 1 (PAR1) increases in the inflammatory bowel disease. The present study investigated the therapeutic effects of PAR1 antagonism on colitis-associated carcinogenesis.

METHODS: A colitis-associated carcinogenesis model was prepared in mice by treatment with azoxymethane (AOM) and dextran sulfate sodium (DSS). PAR1 antagonist, E5555, was administered in long- and short-term protocol, starting on the day of AOM injection and 1 week after completing AOM/DSS treatment, respectively. The fecal samples were collected for metagenome analysis of gut microbiota. The intestinal myofibroblast of the Crohn's disease patients were used to elucidate underlying cellular mechanisms. Caco-2 cells were used to investigate a possible source of PAR1 agonist proteinases.

RESULTS: AOM/DSS model showed weight loss, diarrhea, tumor development, inflammation, fibrosis, and increased production of inflammatory cytokines. The β-diversity, but not α-diversity, of microbiota significantly differed between AOM/DSS and control mice. E5555 alleviated these pathological changes and altered the microbiota β-diversity in AOM/DSS mice. The thrombin expression was upregulated in tumor and non-tumor areas, while PAR1 mRNA expression was higher in tumor areas compared to non-tumor areas. E5555 inhibited thrombin-triggered elevation of cytosolic Ca[2+] concentration and ERK1/2 phosphorylation, as well as IL6-induced STAT3 phosphorylation in intestinal myofibroblasts. Caco-2 cell-conditioned media contained immunoreactive thrombin, which cleaved the recombinant protein containing the extracellular domain of PAR1 at the thrombin cleavage site.

CONCLUSIONS: PAR1 antagonism is proposed to be a novel therapeutic strategy for treatment of inflammatory bowel disease and it associated carcinogenesis.},
}

@article {pmid38614184,
year = {2024},
author = {Sharma, N and Patel, SN and Rai, AK and Singh, SP},
title = {Biochemical characterization of a novel acid-active endopolygalacturonase for pectin depolymerization, pectic-oligomer production, and fruit juice clarification.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {131565},
doi = {10.1016/j.ijbiomac.2024.131565},
pmid = {38614184},
issn = {1879-0003},
abstract = {Endopolygalacturonases are crucial pectinases known for their efficient and sustainable pectin depolymerization activities. The present study identified a novel gene encoding endopolygalacturonase from an acidic mine tailing metagenome. The putative gene showed a maximum identity of 67.55 % with an uncharacterized peptide sequence from Flavobacterium fluvii. The gene was cloned and expressed in a heterologous host, E. coli. Biochemical characterization of the novel endopolygalacturonase enzyme variant (EPHM) showed maximum activity at 60 °C and at 5.0 pH, while retaining 50 % activity under the temperature and pH range of 20 °C to 70 °C for 6 h, and 3.0 to 10.0 for 3 h, respectively. The enzyme exhibited tolerance to different metal ions. EPHM was characterized for the depolymerization of methylated pectin into pectic oligosaccharides. Further, its utility was established for fruit juice clarification, as endorsed by high transmittance, significant viscosity reduction, and release of reducing sugars in the treated fruit juice samples.},
}

@article {pmid38614128,
year = {2024},
author = {Li, C and Guo, X and He, Y and Wang, J and Hao, J and Liu, X},
title = {Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients.},
journal = {Annals of medicine},
volume = {56},
number = {1},
pages = {2337712},
doi = {10.1080/07853890.2024.2337712},
pmid = {38614128},
issn = {1365-2060},
abstract = {Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.},
}

@article {pmid38614031,
year = {2024},
author = {Wang, C and Mao, Y and Zhang, L and Wei, H and Wang, Z},
title = {Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics.},
journal = {Water research},
volume = {256},
number = {},
pages = {121583},
doi = {10.1016/j.watres.2024.121583},
pmid = {38614031},
issn = {1879-2448},
abstract = {The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R[2] = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.},
}

@article {pmid38613799,
year = {2024},
author = {Zhanbo, Q and Jing, Z and Shugao, H and Yinhang, W and Jian, C and Xiang, Y and Feimin, Z and Jian, L and Xinyue, W and Wei, W and Shuwen, H},
title = {Age and aging process alter the gut microbes.},
journal = {Aging},
volume = {16},
number = {},
pages = {},
doi = {10.18632/aging.205728},
pmid = {38613799},
issn = {1945-4589},
abstract = {BACKGROUND: Gut microbes and age are both factors that influence the development of disease. The community structure of gut microbes is affected by age.

OBJECTIVE: To plot time-dependent gut microbe profiles in individuals over 45 years old and explore the correlation between age and gut microbes.

METHODS: Fecal samples were collected from 510 healthy individuals over 45 years old. Shannon index, Simpson index, Ace index, etc. were used to analyze the diversity of gut microbes. The beta diversity analysis, including non-metric multidimensional scaling (NMDS), was used to analyze community distribution. Linear discriminant analysis (LDA) and random forest (RF) algorithm were used to analyze the differences of gut microbes. Trend analysis was used to plot the abundances of characteristic gut microbes in different ages.

RESULTS: The individuals aged 45-49 had the highest richness of gut bacteria. Fifteen characteristic gut microbes, including Siphoviridae and Bifidobacterium breve, were screened by RF algorithm. The abundance of Ligiactobacillus and Microviridae were higher in individuals older than 65 years. Moreover, the abundance of Blautia_A massiliensis, Lubbockvirus and Enterocloster clostridioformis decreased with age and the abundance of Klebsiella variicola and Prevotella increased with age. The functional genes, such as human diseases and aging, were significantly different among different aged individuals.

CONCLUSIONS: The individuals in different ages have characteristic gut microbes. The changes in community structure of gut microbes may be related to age-induced diseases.},
}

@article {pmid38613781,
year = {2024},
author = {Gheorghe, CE and Leigh, SJ and Tofani, GSS and Bastiaanssen, TFS and Lyte, JM and Gardellin, E and Govindan, A and Strain, C and Martinez-Herrero, S and Goodson, MS and Kelley-Loughnane, N and Cryan, JF and Clarke, G},
title = {The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114079},
doi = {10.1016/j.celrep.2024.114079},
pmid = {38613781},
issn = {2211-1247},
abstract = {Chronic stress disrupts microbiota-gut-brain axis function and is associated with altered tryptophan metabolism, impaired gut barrier function, and disrupted diurnal rhythms. However, little is known about the effects of acute stress on the gut and how it is influenced by diurnal physiology. Here, we used germ-free and antibiotic-depleted mice to understand how microbiota-dependent oscillations in tryptophan metabolism would alter gut barrier function at baseline and in response to an acute stressor. Cecal metabolomics identified tryptophan metabolism as most responsive to a 15-min acute stressor, while shotgun metagenomics revealed that most bacterial species exhibiting rhythmicity metabolize tryptophan. Our findings highlight that the gastrointestinal response to acute stress is dependent on the time of day and the microbiome, with a signature of stress-induced functional alterations in the ileum and altered tryptophan metabolism in the colon.},
}

@article {pmid38613509,
year = {2024},
author = {Uçak, S},
title = {Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy.},
journal = {Chemistry & biodiversity},
volume = {},
number = {},
pages = {e202302120},
doi = {10.1002/cbdv.202302120},
pmid = {38613509},
issn = {1612-1880},
abstract = {One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n:10) and after pre-enrichment (n:10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.},
}

@article {pmid38613119,
year = {2024},
author = {Zhou, Y and Zeng, Y and Wang, R and Pang, J and Wang, X and Pan, Z and Jin, Y and Chen, Y and Yang, Y and Ling, W},
title = {Resveratrol Improves Hyperuricemia and Ameliorates Renal Injury by Modulating the Gut Microbiota.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/nu16071086},
pmid = {38613119},
issn = {2072-6643},
support = {81730090//National Natural Science Foundation of China/ ; 81973022//National Natural Science Foundation of China/ ; },
abstract = {Resveratrol (RES) has been reported to prevent hyperuricemia (HUA); however, its effect on intestinal uric acid metabolism remains unclear. This study evaluated the impact of RES on intestinal uric acid metabolism in mice with HUA induced by a high-fat diet (HFD). Moreover, we revealed the underlying mechanism through metagenomics, fecal microbiota transplantation (FMT), and 16S ribosomal RNA analysis. We demonstrated that RES reduced the serum uric acid, creatinine, urea nitrogen, and urinary protein levels, and improved the glomerular atrophy, unclear renal tubule structure, fibrosis, and renal inflammation. The results also showed that RES increased intestinal uric acid degradation. RES significantly changed the intestinal flora composition of HFD-fed mice by enriching the beneficial bacteria that degrade uric acid, reducing harmful bacteria that promote inflammation, and improving microbial function via the upregulation of purine metabolism. The FMT results further showed that the intestinal microbiota is essential for the effect of RES on HUA, and that Lactobacillus may play a key role in this process. The present study demonstrated that RES alleviates HFD-induced HUA and renal injury by regulating the gut microbiota composition and the metabolism of uric acid.},
}

@article {pmid38613058,
year = {2024},
author = {Lombardi, M and Troisi, J and Motta, BM and Torre, P and Masarone, M and Persico, M},
title = {Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/nu16071025},
pmid = {38613058},
issn = {2072-6643},
abstract = {Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.},
}

@article {pmid38612976,
year = {2024},
author = {Fagunwa, O and Davies, K and Bradbury, J},
title = {The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/nu16070942},
pmid = {38612976},
issn = {2072-6643},
support = {FMoH/PTDF//Federal Government of Nigeria/ ; NA//University of Huddersfield/ ; publishing//Queen's University Belfast/ ; },
abstract = {The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.},
}

@article {pmid38612922,
year = {2024},
author = {Neagu, AN and Bruno, P and Johnson, KR and Ballestas, G and Darie, CC},
title = {Biological Basis of Breast Cancer-Related Disparities in Precision Oncology Era.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
doi = {10.3390/ijms25074113},
pmid = {38612922},
issn = {1422-0067},
support = {R15CA260126/CA/NCI NIH HHS/United States ; },
abstract = {Precision oncology is based on deep knowledge of the molecular profile of tumors, allowing for more accurate and personalized therapy for specific groups of patients who are different in disease susceptibility as well as treatment response. Thus, onco-breastomics is able to discover novel biomarkers that have been found to have racial and ethnic differences, among other types of disparities such as chronological or biological age-, sex/gender- or environmental-related ones. Usually, evidence suggests that breast cancer (BC) disparities are due to ethnicity, aging rate, socioeconomic position, environmental or chemical exposures, psycho-social stressors, comorbidities, Western lifestyle, poverty and rurality, or organizational and health care system factors or access. The aim of this review was to deepen the understanding of BC-related disparities, mainly from a biomedical perspective, which includes genomic-based differences, disparities in breast tumor biology and developmental biology, differences in breast tumors' immune and metabolic landscapes, ecological factors involved in these disparities as well as microbiomics- and metagenomics-based disparities in BC. We can conclude that onco-breastomics, in principle, based on genomics, proteomics, epigenomics, hormonomics, metabolomics and exposomics data, is able to characterize the multiple biological processes and molecular pathways involved in BC disparities, clarifying the differences in incidence, mortality and treatment response for different groups of BC patients.},
}

@article {pmid38612702,
year = {2024},
author = {McDermott, G and Walsh, A and Crispie, F and Frost, S and Greally, P and Cotter, PD and O'Sullivan, O and Renwick, J},
title = {Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
doi = {10.3390/ijms25073893},
pmid = {38612702},
issn = {1422-0067},
support = {204814/Z/16/A/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.},
}

@article {pmid38612577,
year = {2024},
author = {Feng, C and Li, N and Gao, G and He, Q and Kwok, LY and Zhang, H},
title = {Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
doi = {10.3390/ijms25073768},
pmid = {38612577},
issn = {1422-0067},
support = {NDYB2022-41//Research Initiation Project for Introducing Excellent Doctoral Talents from Inner Mongolia Agricultural University/ ; 2022YFD2100700//Research Fund for the National Key R&D Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; CARS36//earmarked fund/ ; },
abstract = {The gut microbiota plays a significant role in tumor pathogenesis by regulating the host metabolism and immune response, and there are few studies focused on tracking changes in the gut microbiota from the onset of lung cancer. Therefore, the aim of our study is combining preclinical and clinical research to thoroughly analyze the signatures of fecal microbiota in lung cancer, which will be useful for early diagnosis and predicting the therapeutic efficacy of lung cancer. The first part of this study analyzed the fecal metagenomic differences between patients with non-small cell lung cancer and healthy subjects, and the second part of this work constructed a murine lung cancer model to monitor changes in mouse fecal metagenomics and T cell immunology during lung cancer progression. We found that the fecal microbiota was altered in both humans and mice with lung cancer, characterized by a significantly reduced microbial diversity and number of beneficial microbes, with increases in potential pathogens. The fecal level of Akkermansia muciniphila and the gut metabolic module of the secondary bile acid metabolism were diminished in both humans and mice with lung cancer compared with healthy subjects. Splenomegaly was observed in the lung cancer mice. Flow cytometer analysis of the splenocytes revealed substantial alterations in the proportions of T cell subsets in the lung cancer mice, characterized by significant increases in CD4[+]Foxp3[+]CD25[+] T regulatory cells (p < 0.05) while significant decreases in CD3[+] T cells (p < 0.001), CD4[+] T cells (p < 0.001), and the CD4[+]/CD8[+] ratio (p < 0.01). Vertical and longitudinal analyses of the fecal microbiota of the two mouse groups identified some lung cancer biomarkers (including Acutalibacter timonensis, Lachnospiraceae bacterium NSJ-38 sp014337195, etc.). The fecal microbiota of the lung cancer mice had a reduced metagenomic potential for neurotransmitters (melatonin, γ-aminobutyric acid, and histamine) compared with healthy mice. In summary, this study found that the diversity, structure, and composition of gut microbiota vary between cancer and healthy conditions, ultimately leading to changes in the potential for functional metagenomics.},
}

@article {pmid38612511,
year = {2024},
author = {Parra, M and Aldabaldetrecu, M and Arce, P and Soto-Aguilera, S and Vargas, R and Guerrero, J and Tello, M and Modak, B},
title = {[Cu(NN1)2]ClO4, a Copper (I) Complex as an Antimicrobial Agent for the Treatment of Piscirickettsiosis in Atlantic Salmon.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
doi = {10.3390/ijms25073700},
pmid = {38612511},
issn = {1422-0067},
support = {VIU 21P0017//Agencia Nacional de Investigación y Desarrollo/ ; DICYT022341MC//University of Santiago Chile/ ; DICYT 022343TR//University of Santiago Chile/ ; },
abstract = {Piscirickettsia salmonis is the pathogen that most affects the salmon industry in Chile. Large quantities of antibiotics have been used to control it. In search of alternatives, we have developed [Cu(NN1)2]ClO4 where NN1 = 6-((quinolin-2-ylmethylene)amino)-2H-chromen-2-one. The antibacterial capacity of [Cu(NN1)2]ClO4 was determined. Subsequently, the effect of the administration of [Cu(NN1)2]ClO4 on the growth of S. salar, modulation of the immune system and the intestinal microbiota was studied. Finally, the ability to protect against a challenge with P. salmonis was evaluated. The results obtained showed that the compound has an MIC between 15 and 33.9 μg/mL in four isolates. On the other hand, the compound did not affect the growth of the fish; however, an increase in the transcript levels of IFN-γ, IL-12, IL-1β, CD4, lysozyme and perforin was observed in fish treated with 40 μg/g of fish. Furthermore, modulation of the intestinal microbiota was observed, increasing the genera of beneficial bacteria such as Lactobacillus and Bacillus as well as potential pathogens such as Vibrio and Piscirickettsia. Finally, the treatment increased survival in fish challenged with P. salmonis by more than 60%. These results demonstrate that the compound is capable of protecting fish against P. salmonis, probably by modulating the immune system and the composition of the intestinal microbiota.},
}

@article {pmid38611776,
year = {2024},
author = {Szulc, J and Okrasa, M and Nowak, A and Ryngajłło, M and Nizioł, J and Kuźniar, A and Ruman, T and Gutarowska, B},
title = {Uncontrolled Post-Industrial Landfill-Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment-A Case Study.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {7},
pages = {},
doi = {10.3390/molecules29071496},
pmid = {38611776},
issn = {1420-3049},
support = {Phase IV of the National Program "Safety and working conditions improvement"//Ministry of Science and Higher Education and the National Centre for Research and Development/ ; 726/BN/D/2019-2021//Regional Found for Environmental Protection and Water Management in Lodz/ ; },
abstract = {The aim of this case study was the evaluation of the selected metals' concentration, potential toxic compound identification, cytotoxicity analysis, estimation of the airborne dust concentration, biodiversity, and number of microorganisms in the environment (leachate, soil, air) of the biggest uncontrolled post-industrial landfills in Poland. Based on the results obtained, preliminary solutions for the future management of post-industrial objects that have become an uncontrolled landfill were indicated. In the air, the PM1 fraction dominated, constituting 78.1-98.2% of the particulate matter. Bacterial counts were in the ranges of 9.33 × 10[1]-3.21 × 10[3] CFU m[-3] (air), 1.87 × 10[5]-2.30 × 10[6] CFU mL[-1] (leachates), and 8.33 × 10[4]-2.69 × 10[6] CFU g[-1] (soil). In the air, the predominant bacteria were Cellulosimicrobium and Stenotrophomonas. The predominant fungi were Mycosphaerella, Cladosporium, and Chalastospora. The main bacteria in the leachates and soils were Acinetobacter, Mortierella, Proteiniclasticum, Caloramator, and Shewanella. The main fungi in the leachates and soils were Lindtneria. Elevated concentrations of Pb, Zn, and Hg were detected. The soil showed the most pronounced cytotoxic potential, with rates of 36.55%, 63.08%, and 100% for the A-549, Caco-2, and A-549 cell lines. Nine compounds were identified which may be responsible for this cytotoxic effect, including 2,4,8-trimethylquinoline, benzo(f)quinoline, and 1-(m-tolyl)isoquinoline. The microbiome included bacteria and fungi potentially metabolizing toxic compounds and pathogenic species.},
}

@article {pmid38611599,
year = {2024},
author = {Tsang, HF and Cheung, YS and Yu, CA and Chan, CS and Wong, CT and Yim, KA and Pei, X and Wong, SC},
title = {Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/diagnostics14070686},
pmid = {38611599},
issn = {2075-4418},
support = {RGCQ71P//Research Grants Council HK/ ; UIM/354//HK Innovation and Technology Fund University-Industry Collaborative Programme/ ; },
abstract = {BACKGROUND: Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women.

METHOD: Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed.

RESULTS: MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing.

CONCLUSIONS: In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women's health.},
}

@article {pmid38611483,
year = {2024},
author = {Rojas-Sánchez, B and Castelán-Sánchez, H and Garfias-Zamora, EY and Santoyo, G},
title = {Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/plants13070954},
pmid = {38611483},
issn = {2223-7747},
abstract = {Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.},
}

@article {pmid38611432,
year = {2024},
author = {Papadimitriou, K and Georgalaki, M and Anastasiou, R and Alexandropoulou, AM and Manolopoulou, E and Zoumpopoulou, G and Tsakalidou, E},
title = {Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/foods13071129},
pmid = {38611432},
issn = {2304-8158},
abstract = {Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.},
}

@article {pmid38611328,
year = {2024},
author = {Tsouggou, N and Slavko, A and Tsipidou, O and Georgoulis, A and Dimov, SG and Yin, J and Vorgias, CE and Kapolos, J and Papadelli, M and Papadimitriou, K},
title = {Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/foods13071023},
pmid = {38611328},
issn = {2304-8158},
support = {MIS 5047289//European Union and Greek national funds/ ; },
abstract = {Sfela is a white brined Greek cheese of protected designation of origin (PDO) produced in the Peloponnese region from ovine, caprine milk, or a mixture of the two. Despite the PDO status of Sfela, very few studies have addressed its properties, including its microbiology. For this reason, we decided to investigate the microbiome of two PDO industrial Sfela cheese samples along with two non-PDO variants, namely Sfela touloumotiri and Xerosfeli. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), 16S rDNA amplicon sequencing and shotgun metagenomics analysis were used to identify the microbiome of these traditional cheeses. Cultured-based analysis showed that the most frequent species that could be isolated from Sfela cheese were Enterococcus faecium, Lactiplantibacillus plantarum, Levilactobacillus brevis, Pediococcus pentosaceus and Streptococcus thermophilus. Shotgun analysis suggested that in industrial Sfela 1, Str. thermophilus dominated, while industrial Sfela 2 contained high levels of Lactococcus lactis. The two artisanal samples, Sfela touloumotiri and Xerosfeli, were dominated by Tetragenococcus halophilus and Str. thermophilus, respectively. Debaryomyces hansenii was the only yeast species with abundance > 1% present exclusively in the Sfela touloumotiri sample. Identifying additional yeast species in the shotgun data was challenging, possibly due to their low abundance. Sfela cheese appears to contain a rather complex microbial ecosystem and thus needs to be further studied and understood. This might be crucial for improving and standardizing both its production and safety measures.},
}

@article {pmid38610059,
year = {2024},
author = {Liu, Y and Lin, J},
title = {Periprosthetic bacterial and fugal infection after total knee arthroplasty with one-stage debridement: a case report.},
journal = {Journal of medical case reports},
volume = {18},
number = {1},
pages = {177},
pmid = {38610059},
issn = {1752-1947},
abstract = {BACKGROUND: Periprosthetic infection is a serious complication after arthroplasty and is characterized by a long duration, recurrence, and a low cure rate. Although fungal infections are infrequent, they are often catastrophic, with an insidious onset, a long duration, atypical clinical symptoms, and imaging features in the early stage. They are easily misdiagnosed, or the diagnosis is missed, resulting in wrong treatment approaches.

CASE PRESENTATION: This paper reports a case involving a 62-year-old female patient of Korean ethnicity with a periprosthetic infection after knee arthroplasty who underwent joint debridement. A preoperative metagenomic next-generation sequencing of joint aspirate revealed Staphylococcus epidermidis. However, postsurgical tissue cultures confirmed the fungal infection. The patient received oral voriconazole and intra-articular injection of voriconazole for antifungal treatment. Since bacterial infection could not be ruled out, we also prescribed levofloxacin. No infection recurrence was observed after more than 22 months of follow-up. In the treatment of this patient, successful short-term follow-up was achieved, but long-term efficacy still cannot be determined.

CONCLUSIONS: In addition to the case study, we provide an analysis of the diagnosis and treatment of fungal infection after arthroplasty, especially the efficacy of debridement, antibiotics, and implant retention for a short-term outcome.},
}

@article {pmid38609443,
year = {2024},
author = {Kholousi Adab, F and Mehdi Yaghoobi, M and Gharechahi, J},
title = {Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8560},
pmid = {38609443},
issn = {2045-2322},
abstract = {Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.},
}

@article {pmid38609404,
year = {2024},
author = {Lim, FS and González-Cabrera, J and Keilwagen, J and Kleespies, RG and Jehle, JA and Wennmann, JT},
title = {Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8525},
pmid = {38609404},
issn = {2045-2322},
abstract = {Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.},
}

@article {pmid38609359,
year = {2024},
author = {Han, P and Tang, X and Koch, H and Dong, X and Hou, L and Wang, D and Zhao, Q and Li, Z and Liu, M and Lücker, S and Shi, G},
title = {Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3143},
pmid = {38609359},
issn = {2041-1723},
support = {42276243//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42371064//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42230505//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3[-]) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3[-] via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via [13]C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.},
}

@article {pmid38609235,
year = {2024},
author = {Hou, Q and Wang, Y and Qu, D and Zhao, H and Tian, L and Zhou, J and Liu, J and Guo, Z},
title = {Microbial communities, functional, and flavor differences among three different-colored high-temperature Daqu: A comprehensive metagenomic, physicochemical, and electronic sensory analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {184},
number = {},
pages = {114257},
doi = {10.1016/j.foodres.2024.114257},
pmid = {38609235},
issn = {1873-7145},
abstract = {High-temperature Daqu (HTD) is the starter for producing sauce-flavor Baijiu, with different-colored Daqu (white, yellow, and black) reflecting variations in fermentation chamber conditions, chemical reactions, and associated microbiota. Understanding the relationship between Daqu characteristics and flavor/taste is challenging yet vital for improving Baijiu fermentation. This study utilized metagenomic sequencing, physicochemical analysis, and electronic sensory evaluation to compare three different-colored HTD and their roles in fermentation. Fungi and bacteria dominated the HTD-associated microbiota, with fungi increasing as the fermentation temperature rose. The major fungal genera were Aspergillus (40.17%) and Kroppenstedtia (21.16%), with Aspergillus chevalieri (25.65%) and Kroppenstedtia eburnean (21.07%) as prevalent species. Microbial communities, functionality, and physicochemical properties, particularly taste and flavor, were color-specific in HTD. Interestingly, the microbial communities in different-colored HTDs demonstrated robust functional complementarity. White Daqu exhibited non-significantly higher α-diversity compared to the other two Daqu. It played a crucial role in breaking down substrates such as starch, proteins, hyaluronic acid, and glucan, contributing to flavor precursor synthesis. Yellow Daqu, which experienced intermediate temperature and humidity, demonstrated good esterification capacity and a milder taste profile. Black Daqu efficiently broke down raw materials, especially complex polysaccharides, but had inferior flavor and taste. Notably, large within-group variations in physicochemical quality and microbial composition were observed, highlighting limitations in color-based HTD quality assessment. Water content in HTD was associated with Daqu flavor, implicating its crucial role. This study revealed the complementary roles of the three HTD types in sauce-flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}

@article {pmid38609223,
year = {2024},
author = {Ma, J and Qian, C and Hu, Q and Zhang, J and Gu, G and Liang, X and Zhang, L},
title = {The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {184},
number = {},
pages = {114244},
doi = {10.1016/j.foodres.2024.114244},
pmid = {38609223},
issn = {1873-7145},
abstract = {Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.},
}

@article {pmid38608888,
year = {2024},
author = {Feng, K and Lu, Y and Zhou, W and Xu, Z and Ye, J and Zhang, S and Chen, J and Zhao, J},
title = {Metagenomics revealing biomolecular insights into the enhanced toluene removal and electricity generation in PANI@CNT bioanode.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172402},
doi = {10.1016/j.scitotenv.2024.172402},
pmid = {38608888},
issn = {1879-1026},
abstract = {Microbial fuel cells (MFCs) have significant potential for environmental remediation and energy recycling directly from refractory aromatic hydrocarbons. To boost the capacities of toluene removal and the electricity production in MFCs, this study constructed a polyaniline@carbon nanotube (PANI@CNT) bioanode with a three-dimensional framework structure. Compared with the control bioanode based on graphite sheet, the PANI@CNT bioanode increased the output voltage and toluene degradation kinetics by 2.27-fold and 1.40-fold to 0.399 V and 0.60 h[-1], respectively. Metagenomic analysis revealed that the PANI@CNT bioanode promoted the selective enrichment of Pseudomonas, with the dual functions of degrading toluene and generating exogenous electrons. Additionally, compelling genomic evidence elucidating the relationship between functional genes and microorganisms was found. It was interesting that the genes derived from Pseudomonas related to extracellular electron transfer, tricarboxylic acid cycle, and toluene degradation were upregulated due to the existence of PANI@CNT. This study provided biomolecular insights into key genes and related microorganisms that effectively facilitated the organic pollutant degradation and energy recovery in MFCs, offering a novel alternative for high-performance bioanode.},
}

@article {pmid38608842,
year = {2024},
author = {Sun, Z and Ning, Z and Figeys, D},
title = {The Landscape and Perspectives of the Human Gut Metaproteomics.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {100763},
doi = {10.1016/j.mcpro.2024.100763},
pmid = {38608842},
issn = {1535-9484},
abstract = {The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this paper, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from fifteen published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.},
}

@article {pmid38608741,
year = {2024},
author = {Kebede, V and Ravizza, T and Balosso, S and Di Sapia, R and Canali, L and Soldi, S and Galletti, S and Papazlatani, C and Karas, PA and Vasileiadis, S and Sforzini, A and Pasetto, L and Bonetto, V and Vezzani, A and Vesci, L},
title = {Early treatment with rifaximin during epileptogenesis reverses gut alterations and reduces seizure duration in a mouse model of acquired epilepsy.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.04.007},
pmid = {38608741},
issn = {1090-2139},
abstract = {The gut microbiota is altered in epilepsy and is emerging as a potential target for new therapies. We studied the effects of rifaximin, a gastrointestinal tract-specific antibiotic, on seizures and neuropathology and on alterations in the gut and its microbiota in a mouse model of temporal lobe epilepsy (TLE). Epilepsy was induced by intra-amygdala kainate injection causing status epilepticus (SE) in C57Bl6 adult male mice. Sham mice were injected with vehicle. Two cohorts of SE mice were fed a rifaximin-supplemented diet for 21 days, starting either at 24 h post-SE (early disease stage) or at day 51 post-SE (chronic disease stage). Corresponding groups of SE mice (one each disease stage) were fed a standard (control) diet. Cortical ECoG recording was done at each disease stage (24/7) for 21 days in all SE mice to measure the number and duration of spontaneous seizures during either rifaximin treatment or control diet. Then, epileptic mice ± rifaximin and respective sham mice were sacrificed and brain, gut and feces collected. Biospecimens were used for: (i) quantitative histological analysis of the gut structural and cellular components; (ii) markers of gut inflammation and intestinal barrier integrity by RTqPCR; (iii) 16S rRNA metagenomics analysis in feces. Hippocampal neuronal cell loss was assessed in epileptic mice killed in the early disease phase. Rifaximin administered for 21 days post-SE (early disease stage) reduced seizure duration (p < 0.01) and prevented hilar mossy cells loss in the hippocampus compared to epileptic mice fed a control diet. Epileptic mice fed a control diet showed a reduction of both villus height and villus/crypt depth ratio (p < 0.01) and a decreased number of goblet cells (p < 0.01) in the duodenum, as well as increased macrophage (Iba1)-immunostaining in the jejunum (p < 0.05), compared to respective sham mice. Rifaximin's effect on seizures was associated with a reversal of gut structural and cellular changes, except for goblet cells which remained reduced. Seizure duration in epileptic mice was negatively correlated with the number of mossy cells (p < 0.01) and with villus height/crypt depth ratio (p < 0.05). Rifaximin-treated epileptic mice also showed increased tight junctions (occludin and ZO-1, p < 0.01) and decreased TNF mRNA expression (p < 0.01) in the duodenum compared to epileptic mice fed a control diet. Rifaximin administered for 21 days in chronic epileptic mice (chronic disease stage) did not change the number or duration of seizures compared to epileptic mice fed a control diet. Chronic epileptic mice fed a control diet showed an increased crypt depth (p < 0.05) and reduced villus height/crypt depth ratio (p < 0.01) compared to respective sham mice. Rifaximin treatment did not affect these intestinal changes. At both disease stages, rifaximin modified α- and β-diversity in epileptic and sham mice compared to respective mice fed a control diet. The microbiota composition in epileptic mice, as well as the effects of rifaximin at the phylum, family and genus levels, depended on the stage of the disease. During the early disease phase, the abundance of specific taxa was positively correlated with seizure duration in epileptic mice. In conclusion, gut-related alterations reflecting a dysfunctional state, occur during epilepsy development in a TLE mouse model. A short-term treatment with rifaximin during the early phase of the disease, reduced seizure duration and neuropathology, and reversed some intestinal changes, strengthening the therapeutic effects of gut-based therapies in epilepsy.},
}

@article {pmid38608237,
year = {2024},
author = {Downie, DL and Rao, P and David-Ferdon, C and Courtney, S and Lee, JS and Kugley, S and MacDonald, PDM and Barnes, K and Fisher, S and Andreadis, JL and Chaitram, J and Mauldin, MR and Salerno, RM and Schiffer, J and Gundlapalli, AV},
title = {Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health.},
journal = {Health security},
volume = {},
number = {},
pages = {},
doi = {10.1089/hs.2023.0100},
pmid = {38608237},
issn = {2326-5108},
abstract = {To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.},
}

@article {pmid38608141,
year = {2024},
author = {Hunt, KA and Carr, AV and Otwell, AE and Valenzuela, JJ and Walker, KS and Dixon, ER and Lui, LM and Nielsen, TN and Bowman, S and von Netzer, F and Moon, JW and Schadt, CW and Rodriguez, M and Lowe, K and Joyner, D and Davis, KJ and Wu, X and Chakraborty, R and Fields, MW and Zhou, J and Hazen, TC and Arkin, AP and Wankel, SD and Baliga, NS and Stahl, DA},
title = {Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c07972},
pmid = {38608141},
issn = {1520-5851},
abstract = {The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.},
}

@article {pmid38606356,
year = {2024},
author = {Monger, XC and Saucier, L and Guay, F and Turcotte, A and Lemieux, J and Pouliot, E and Fournaise, S and Vincent, AT},
title = {Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1355134},
pmid = {38606356},
issn = {1664-8021},
abstract = {Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower[®] PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.},
}

@article {pmid38606341,
year = {2024},
author = {Eitel, M and Osigus, HJ and Brenzinger, B and Wörheide, G},
title = {Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11220},
pmid = {38606341},
issn = {2045-7758},
abstract = {The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.},
}

@article {pmid38606292,
year = {2024},
author = {Jiang, Z and Gai, W and Zhang, X and Zheng, Y and Jin, X and Han, Z and Ao, G and He, J and Shu, D and Liu, X and Zhou, Y and Hua, Z},
title = {Clinical performance of metagenomic next-generation sequencing for diagnosis of pulmonary Aspergillus infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1345706},
pmid = {38606292},
issn = {2235-2988},
abstract = {BACKGROUND: Investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguish Aspergillus infection from colonization are currently insufficient.

METHODS: The performance of mNGS in distinguishing Aspergillus infection from colonization, along with the differences in patients' characteristics, antibiotic adjustment, and lung microbiota, were analyzed.

RESULTS: The abundance of Aspergillus significantly differed between patients with Aspergillus infection (n=36) and colonization (n=32) (P < 0.0001). Receiver operating characteristic (ROC) curve result for bronchoalveolar lavage fluid (BALF) mNGS indicated an area under the curve of 0.894 (95%CI: 0.811-0.976), with an optimal threshold value of 23 for discriminating between Aspergillus infection and colonization. The infection group exhibited a higher proportion of antibiotic adjustments in comparison to the colonization group (50% vs. 12.5%, P = 0.001), with antibiotic escalation being more dominant. Age, length of hospital stay, hemoglobin, cough and chest distress were significantly positively correlated with Aspergillus infection. The abundance of A. fumigatus and Epstein-Barr virus (EBV) significantly increased in the infection group, whereas the colonization group exhibited higher abundance of A. niger.

CONCLUSION: BALF mNGS is a valuable tool for differentiating between colonization and infection of Aspergillus. Variations in patients' age, length of hospital stay, hemoglobin, cough and chest distress are observable between patients with Aspergillus infection and colonization.},
}

@article {pmid38605646,
year = {2024},
author = {Heston, SM and Hurst, JH and Kelly, MS},
title = {Understanding the influence of the microbiome on childhood infections.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/14787210.2024.2340664},
pmid = {38605646},
issn = {1744-8336},
abstract = {INTRODUCTION: The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED: In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION: Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.},
}

@article {pmid38605401,
year = {2024},
author = {Feng, X and Li, H},
title = {Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {92},
pmid = {38605401},
issn = {1474-760X},
support = {R01HG010040/HG/NHGRI NIH HHS/United States ; U01HG010961/HG/NHGRI NIH HHS/United States ; },
abstract = {BACKGROUND: In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.

RESULTS: Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.

CONCLUSIONS: Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.},
}

@article {pmid38604482,
year = {2024},
author = {Chang, H and Du, B and He, K and Yin, Q and Wu, G},
title = {Mechanistic understanding of acclimation and energy metabolism of acetoclastic methanogens under different substrate to microorganism ratios.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118911},
doi = {10.1016/j.envres.2024.118911},
pmid = {38604482},
issn = {1096-0953},
abstract = {Mechanistic understanding of acetoclastic methanogenesis is pivotal for optimizing anaerobic digestion for efficient methane production. In this study, two different operational modes, continuous flow reactor (CFR) and sequencing batch reactor (SBR), accompanied with solids retention times (SRT) of 10 days (SBR10d and CFR10d) and 25 days (SBR25d and CFR25d) were implemented to elucidate their impacts on microbial communities and energy metabolism of methanogens in acetate-fed systems. Microbial community analysis revealed that the relative abundance of Methanosarcina (16.0% ∼ 46.0%) surpassed Methanothrix (3.7% ∼ 22.9%) in each reactor. SBRs had the potential to enrich both Methanothrix and Methanosarcina. Compared to SBRs, CFRs had lower total relative abundance of methanogens. Methanosarcina exhibited a superior enrichment in reactors with 10-day SRT, while Methanothrix preferred to be acclimated in reactors with 25-day SRT. The operational mode and SRT were also observed to affect the distribution of acetate-utilizing bacteria, including Pseudomonas, Desulfocurvus, Mesotoga, and Thauera. Regarding enzymes involved in energy metabolism, Ech and Vho/Vht demonstrated higher relative abundances at 10-day SRT compared to 25-day SRT, whereas Fpo and MtrA-H showed higher relative abundances in SBRs than those in CFRs. The relative abundance of genes encoding ATPase harbored by Methanothrix was higher than Methanosarcina at 25-day SRT. Additionally, the relative abundance of V/A-type ATPase (typically for methanogens) was observed higher in SBRs compared to CFRs, while the F-type ATPase (typically for bacteria) exhibited higher relative abundance in CFRs than that in SBRs.},
}

@article {pmid38604355,
year = {2024},
author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L},
title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172251},
doi = {10.1016/j.scitotenv.2024.172251},
pmid = {38604355},
issn = {1879-1026},
abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.},
}

@article {pmid38603815,
year = {2024},
author = {Bai, H and He, LY and Gao, FZ and Yao, KS and Zhang, M and Qiao, LK and Chen, ZY and He, LX and Liu, YS and Zhao, JL and Ying, GG},
title = {Airborne antibiotic resistome and microbiome in pharmaceutical factories.},
journal = {Environment international},
volume = {186},
number = {},
pages = {108639},
doi = {10.1016/j.envint.2024.108639},
pmid = {38603815},
issn = {1873-6750},
abstract = {Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.},
}

@article {pmid38602400,
year = {2024},
author = {Shcherbakova, VA and Rechkina, VI and Trubitsyn, VE},
title = {Metagenome-assembled genomes of the methanogenic enrichment obtained from drilling fluid wastes stored in permafrost.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0115923},
doi = {10.1128/mra.01159-23},
pmid = {38602400},
issn = {2576-098X},
abstract = {We studied methanogenic enrichment (Kha) from spent drilling fluid stored in permafrost, Kharasavey (71°10'50″N 66°51'50″E) gas field located in the western part of the Yamal Peninsula. The metagenome-assembled genomes showed that Kha consists of representatives of Methanosarcina, Methanobacterium, Proteinifillum, and Synergistetes genera.},
}

@article {pmid38601940,
year = {2024},
author = {Sohaib, H and Fays, M and Khatib, A and Rivière, J and El Aouad, N and Desoignies, N},
title = {Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1310395},
pmid = {38601940},
issn = {1664-302X},
abstract = {Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte-host interactions shape argan adaptation across Morocco's diverse landscapes.},
}

@article {pmid38601936,
year = {2024},
author = {Ortañez, J and Degnan, PH},
title = {Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1241582},
pmid = {38601936},
issn = {1664-302X},
abstract = {The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.},
}