@article {pmid38714759,
year = {2024},
author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R},
title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38714759},
issn = {2058-5276},
support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
}

@article {pmid38714760,
year = {2024},
author = {Jamiu, A and Chaguza, C},
title = {Metagenomics to improve infectious disease diagnostics in low- and middle-income countries.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38714760},
issn = {2058-5276},
}

@article {pmid38714231,
year = {2024},
author = {Wang, YL and Ikuma, K and Brown, AMV and Deonarine, A},
title = {Global survey of hgcA-carrying genomes in marine and freshwater sediments: Insights into mercury methylation processes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124117},
doi = {10.1016/j.envpol.2024.124117},
pmid = {38714231},
issn = {1873-6424},
abstract = {Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman's correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.},
}

@article {pmid38714217,
year = {2024},
author = {Martinez-Fajardo, C and Navarro-Simarro, P and Morote, L and Rubio-Moraga, Á and Mondejar-López, M and Niza, E and Argandoña, J and Ahrazem, O and Gómez-Gómez, L and López-Jimenez, AJ},
title = {"Exploring the Viral Landscape of Saffron through Metatranscriptomic Analysis.".},
journal = {Virus research},
volume = {},
number = {},
pages = {199389},
doi = {10.1016/j.virusres.2024.199389},
pmid = {38714217},
issn = {1872-7492},
abstract = {Saffron (Crocus sativus L.), a historically significant crop valued for its nutraceutical properties, has been poorly explored from a phytosanitary perspective. This study conducted a thorough examination of viruses affecting saffron samples from Spanish cultivars, using high-throughput sequencing alongside a systematic survey of transcriptomic datasets from Crocus sativus at the Sequence Read Archive. Our analysis unveiled a broad diversity and abundance, identifying 17 viruses across the 52 analyzed libraries, some of which were highly prevalent. This includes known saffron-infecting viruses and previously unreported ones. In addition, we discovered 7 novel viruses from the Alphaflexiviridae, Betaflexiviridae, Potyviridae, Solemoviridae, and Geminiviridae families, with some present in libraries from various locations. These findings indicate that the saffron-associated virome is more complex than previously reported, emphasizing the potential of phytosanitary analysis to enhance saffron productivity.},
}

@article {pmid38714055,
year = {2024},
author = {Li, Z and Wang, J and Yue, H and Rehman, A and Yousaf, M and Du, M and Zhang, X},
title = {Applying metabolic modeling and multi-omics to elucidate the biotransformation mechanisms of marine algal toxin domoic acid (DA) in sediments.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134541},
doi = {10.1016/j.jhazmat.2024.134541},
pmid = {38714055},
issn = {1873-3336},
abstract = {Domoic acid (DA)-producing algal blooms are a global marine environmental issue. However, there has been no previous research addressing the question regarding the fate of DA in marine benthic environments. In this work, we investigated the DA fate in the water-sediment microcosm via the integrative analysis of a top-down metabolic model, metagenome, and metabolome. Results demonstrated that biodegradation is the leading mechanism for the nonconservative attenuation of DA. Specifically, DA degradation was prominently completed by the sediment aerobic community, with a degradation rate of 0.0681 ± 0.00954 d[-1]. The DA degradation pathway included hydration, dehydrogenation, hydrolysis, decarboxylation, automatic ring opening of hydration, and β oxidation reactions. Moreover, the reverse ecological analysis demonstrated that the microbial community transitioned from nutrient competition to metabolic cross-feeding during DA degradation, further enhancing the cooperation between DA degraders and other taxa. Finally, we reconstructed the metabolic process of microbial communities during DA degradation and confirmed that the metabolism of amino acid and organic acid drove the degradation of DA. Overall, our work not only elucidated the fate of DA in marine environments but also provided crucial insights for applying metabolic models and multi-omics to investigate the biotransformation of other contaminants.},
}

@article {pmid38713622,
year = {2024},
author = {Torcello-Requena, A and Murphy, ARJ and Lidbury, IDEA and Pitt, FD and Stark, R and Millard, AD and Puxty, RJ and Chen, Y and Scanlan, DJ},
title = {A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {20},
pages = {e2312892121},
doi = {10.1073/pnas.2312892121},
pmid = {38713622},
issn = {1091-6490},
support = {NE/I00985X/1//UKRI | Natural Environment Research Council (NERC)/ ; 883551//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {*Alkaline Phosphatase/metabolism/genetics ; *Prochlorococcus/genetics/metabolism ; Phosphorus/metabolism ; Bacterial Proteins/metabolism/genetics ; Synechococcus/genetics/metabolism ; Phylogeny ; Seawater/microbiology ; },
abstract = {Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.},
}

*Alkaline Phosphatase/metabolism/genetics
*Prochlorococcus/genetics/metabolism
Phosphorus/metabolism
Bacterial Proteins/metabolism/genetics
Synechococcus/genetics/metabolism
Phylogeny
Seawater/microbiology

@article {pmid38713374,
year = {2024},
author = {Rawat, M and Chauhan, M and Pandey, A},
title = {Extremophiles and their expanding biotechnological applications.},
journal = {Archives of microbiology},
volume = {206},
number = {6},
pages = {247},
pmid = {38713374},
issn = {1432-072X},
mesh = {*Extremophiles/metabolism ; *Biotechnology ; *Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics/classification ; *Extreme Environments ; },
abstract = {Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.},
}

*Extremophiles/metabolism
*Biotechnology
*Archaea/metabolism/genetics
*Bacteria/metabolism/genetics/classification
*Extreme Environments

@article {pmid38712931,
year = {2024},
author = {Sim, KH and Ho, J and Lim, JQ and Chan, SH and Li, A and Chng, KR},
title = {A metagenomics-based workflow for the detection and genomic characterization of GBS in raw freshwater fish.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0327623},
doi = {10.1128/spectrum.03276-23},
pmid = {38712931},
issn = {2165-0497},
abstract = {UNLABELLED: The unexpected foodborne outbreak in Singapore in 2015 has accentuated Group B Streptococcus (GBS, Streptococcus agalactiae) sequence type 283 as an emerging foodborne pathogen transmitted via the consumption of contaminated raw freshwater fish. Isolation-based workflows utilizing conventional microbiological and whole-genome sequencing methods are commonly used to support biosurveillance efforts critical for the control management of this emerging foodborne pathogen. However, these isolation-based workflows tend to have relatively long turnaround times that hamper a timely response for implementing risk mitigation. To address this gap, we have developed a metagenomics-based workflow for the simultaneous detection and genomic characterization of GBS in raw freshwater fish. Notably, our validation results showed that this metagenomics-based workflow could achieve comparable accuracy and potentially better detection limits while halving the turnaround time (from 2 weeks to 5 days) relative to an isolation-based workflow. The metagenomics-based workflow was also successfully adapted for use on a portable long-read nanopore sequencer, demonstrating its potential applicability for real-time point-of-need testing. Using GBS in freshwater fish as an example, this work represents a proof-of-concept study that supports the feasibility and validity of metagenomics as a rapid and accurate test methodology for the detection and genomic characterization of foodborne pathogens in complex food matrices.

IMPORTANCE: The need for a rapid and accurate food microbiological testing method is apparent for a timely and effective foodborne outbreak response. This is particularly relevant for emerging foodborne pathogens such as Group B Streptococcus (GBS) whose associated food safety risk might be undercharacterized. By using GBS in raw freshwater fish as a case example, this study describes the development of a metagenomics-based workflow for rapid food microbiological safety testing and surveillance. This study can inform as a working model for various foodborne pathogens in other complex food matrices, paving the way for future methodological development of metagenomics for food microbiological safety testing.},
}

@article {pmid38712927,
year = {2024},
author = {Zhang, S and Swarte, JC and Gacesa, R and Knobbe, TJ and Kremer, D and Jansen, BH and de Borst, MH and , and Harmsen, HJM and Erasmus, ME and Verschuuren, EAM and Bakker, SJL and Gan, CT and Weersma, RK and Björk, JR},
title = {The gut microbiome in end-stage lung disease and lung transplantation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0131223},
doi = {10.1128/msystems.01312-23},
pmid = {38712927},
issn = {2379-5077},
abstract = {Gut dysbiosis has been associated with impaired outcomes in liver and kidney transplant recipients, but the gut microbiome of lung transplant recipients has not been extensively explored. We assessed the gut microbiome in 64 fecal samples from end-stage lung disease patients before transplantation and 219 samples from lung transplant recipients after transplantation using metagenomic sequencing. To identify dysbiotic microbial signatures, we analyzed 243 fecal samples from age-, sex-, and BMI-matched healthy controls. By unsupervised clustering, we identified five groups of lung transplant recipients using different combinations of immunosuppressants and antibiotics and analyzed them in relation to the gut microbiome. Finally, we investigated the gut microbiome of lung transplant recipients in different chronic lung allograft dysfunction (CLAD) stages and longitudinal gut microbiome changes after transplantation. We found 108 species (58.1%) in end-stage lung disease patients and 139 species (74.7%) in lung transplant recipients that were differentially abundant compared with healthy controls, with several species exhibiting sharp longitudinal increases from before to after transplantation. Different combinations of immunosuppressants and antibiotics were associated with specific gut microbial signatures. We found that the gut microbiome of lung transplant recipients in CLAD stage 0 was more similar to healthy controls compared to those in CLAD stage 1. Finally, the gut microbial diversity of lung transplant recipients remained lower than the average gut microbial diversity of healthy controls up to more than 20 years post-transplantation. Gut dysbiosis, already present before lung transplantation was exacerbated following lung transplantation.IMPORTANCEThis study provides extensive insights into the gut microbiome of end-stage lung disease patients and lung transplant recipients, which warrants further investigation before the gut microbiome can be used for microbiome-targeted interventions that could improve the outcome of lung transplantation.},
}

@article {pmid38712467,
year = {2024},
author = {Cao, Y and Du, P and Li, Z and Xu, J and Ma, C and Liang, B},
title = {Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.14903},
pmid = {38712467},
issn = {1365-3040},
support = {C2021204158//Natural Science Foundation of Hebei/ ; 31901964//National Natural Science Foundation of China/ ; CXZZBS2024076//Innovation Ability Training Project for Graduate Student of Hebei Province/ ; HBCT2024150205//Earmarked Fund for Hebei Apple Innovation Team of Modern Agroindustry Technology Research System/ ; CARS-27//Earmarked fund for the China Agricultural Research System/ ; },
abstract = {The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress.},
}

@article {pmid38712258,
year = {2024},
author = {Goldman, SL and Sanders, JG and Sprockett, DD and Landers, A and Yan, W and Moeller, AH},
title = {Hackflex library preparation enables low-cost metagenomic profiling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.23.590092},
pmid = {38712258},
abstract = {Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.},
}

@article {pmid38712063,
year = {2024},
author = {Nyawo, G and Naidoo, C and Wu, BG and Kwok, B and Clemente, JC and Li, Y and Minnies, S and Reeve, B and Moodley, S and John, TJ and Karamchand, S and Singh, S and Pecararo, A and Doubell, A and Kyriakakis, C and Warren, R and Segal, LN and Theron, G},
title = {Bad company? The pericardium microbiome in people investigated for tuberculosis pericarditis in an HIV-prevalent setting.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.26.24306431},
pmid = {38712063},
abstract = {BACKGROUND: The microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive tuberculous pericarditis, a major cause of mortality, and explored for the first time, the interaction between its association with C-reactive protein (CRP), a potential diagnostic biomarker and the site-of-disease microbiome in extrapulmonary TB.

METHODS: People with effusions requiring diagnostic pericardiocentesis (n=139) provided background sampling controls and pericardial fluid (PF) for 16S rRNA gene sequencing analysed using QIIME2 and PICRUSt2. Blood was collected to measure CRP.

RESULTS: PF from people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis differed in β-diversity. dTBs were, vs. nTBs, Mycobacterium-, Lacticigenium-, and Kocuria- enriched. Within dTBs, HIV-positives were Mycobacterium-, Bifidobacterium- , Methylobacterium- , and Leptothrix -enriched vs. HIV-negatives and HIV-positive dTBs on ART were Mycobacterium - and Bifidobacterium -depleted vs. those not on ART. Compared to nTBs, dTBs exhibited short-chain fatty acid (SCFA) and mycobacterial metabolism microbial pathway enrichment. People with additional non-pericardial involvement had differentially PF taxa (e.g., Mycobacterium -enrichment and Streptococcus -depletion associated with pulmonary infiltrates). Mycobacterium reads were in 34% (31/91), 8% (2/25) and 17% (4/23) of dTBs, pTBs, and nTBs, respectively. β-diversity differed between patients with CRP above vs. below the median value (Pseudomonas -depleted). There was no correlation between enriched taxa in dTBs and CRP.

CONCLUSIONS: PF is compositionally distinct based on TB status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance of these findings, including mycobacterial reads in nTBs and pTBs, requires evaluation.},
}

@article {pmid38712043,
year = {2024},
author = {Shobnam, N and Saksena, S and Ratley, G and Yadav, M and Chaudhary, PP and Sun, AA and Howe, KN and Gadkari, M and Franco, LM and Ganesan, S and McCann, KJ and Hsu, AP and Kanakabandi, K and Ricklefs, S and Lack, J and Yu, W and Similuk, M and Walkiewicz, MA and , and Gardner, DD and Barta, K and Tullos, K and Myles, IA},
title = {Topical Steroid Withdrawal is a Targetable Excess of Mitochondrial NAD.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.17.24305846},
pmid = {38712043},
abstract = {BACKGROUND: Topical corticosteroids (TCS) are first-line therapies for numerous skin conditions. Topical Steroid Withdrawal (TSW) is a controversial diagnosis advocated by patients with prolonged TCS exposure who report severe systemic reactions upon treatment cessation. However, to date there have been no systematic clinical or mechanistic studies to distinguish TSW from other eczematous disorders.

METHODS: A re-analysis of a previous survey with eczematous skin disease was performed to evaluate potential TSW distinguishing symptoms. We subsequently conducted a pilot study of 16 patients fitting the proposed diagnostic criteria. We then performed: tissue metabolomics, transcriptomics, and immunostaining on skin biopsies; serum metabolomics and cytokine assessments; shotgun metagenomics on microbiome skin swabs; genome sequencing; followed by functional, mechanistic studies using human skin cell lines and mice.

RESULTS: Clinically distinct TSW symptoms included burning, flushing, and thermodysregulation. Metabolomics and transcriptomics both implicated elevated NAD+ oxidation stemming from increased expression of mitochondrial complex I and conversion of tryptophan into kynurenine metabolites. These abnormalities were induced by glucocorticoid exposure both in vitro and in a cohort of healthy controls (N=19) exposed to TCS. Targeting complex I via either metformin or the herbal compound berberine improved outcomes in both cell culture and in an open-label case series for patients with TSW.

CONCLUSION: Taken together, our results suggest that TSW has a distinct dermatopathology. While future studies are needed to validate these results in larger cohorts, this work provides the first mechanistic evaluation into TSW pathology, and offers insights into clinical identification, pharmacogenomic candidates, and directed therapeutic strategies.},
}

@article {pmid38711860,
year = {2024},
author = {Hou, S and Tang, T and Cheng, S and Liu, Y and Xia, T and Chen, T and Fuhrman, JA and Sun, F},
title = {DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {2},
pages = {lqae044},
pmid = {38711860},
issn = {2631-9268},
abstract = {Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e. viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. DeepMicroClass achieved high performance for all sequence classes at various tested sequence lengths ranging from 500 bp to 100 kbps. By benchmarking on a synthetic dataset with variable sequence class composition, we showed that DeepMicroClass obtained better performance for eukaryotic, plasmid and viral contig classification than other state-of-the-art predictors. DeepMicroClass achieved comparable performance on viral sequence classification with geNomad and VirSorter2 when benchmarked on the CAMI II marine dataset. Using a coastal daily time-series metagenomic dataset as a case study, we showed that microbial eukaryotes and prokaryotic viruses are integral to microbial communities. By analyzing monthly metagenomes collected at HOT and BATS, we found relatively higher viral read proportions in the subsurface layer in late summer, consistent with the seasonal viral infection patterns prevalent in these areas. We expect DeepMicroClass will promote metagenomic studies of under-appreciated sequence types.},
}

@article {pmid38711505,
year = {2024},
author = {Lai, Y and Tang, W and Luo, X and Zheng, H and Zhang, Y and Wang, M and Yu, G and Yang, M},
title = {Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1369116},
pmid = {38711505},
issn = {1664-3224},
mesh = {Humans ; *Spondylitis, Ankylosing/microbiology/metabolism/immunology ; *Gastrointestinal Microbiome ; *Probiotics ; Male ; Female ; *Metabolome ; Adult ; *Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Prospective Studies ; Metabolomics ; Bacteria/metabolism/classification/isolation & purification ; Tumor Necrosis Factor Inhibitors/therapeutic use/pharmacology ; },
abstract = {OBJECTIVE: Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS.

METHODS: To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites.

RESULTS: A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria Ruminococcus gnavus and the promotion of the probiotic bacteria Bacteroides uniformis. Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored.

CONCLUSION: In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.},
}

Humans
*Spondylitis, Ankylosing/microbiology/metabolism/immunology
*Gastrointestinal Microbiome
*Probiotics
Male
Female
*Metabolome
Adult
*Feces/microbiology
Metagenomics/methods
Middle Aged
Prospective Studies
Metabolomics
Bacteria/metabolism/classification/isolation & purification
Tumor Necrosis Factor Inhibitors/therapeutic use/pharmacology

@article {pmid38710918,
year = {2024},
author = {Liu, L and Zhao, M and Lang, X and Jia, S and Kang, X and Liu, Y and Liu, J},
title = {Modified Lichong decoction intervenes in colorectal cancer by modulating the intestinal flora and the Wnt/β-catenin signaling pathway.},
journal = {Journal of cancer research and clinical oncology},
volume = {150},
number = {5},
pages = {234},
pmid = {38710918},
issn = {1432-1335},
mesh = {*Wnt Signaling Pathway/drug effects ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Colorectal Neoplasms/drug therapy/pathology/metabolism ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Humans ; Male ; Apoptosis/drug effects ; Epithelial-Mesenchymal Transition/drug effects ; Cell Proliferation/drug effects ; Dextran Sulfate ; beta Catenin/metabolism ; Disease Models, Animal ; },
abstract = {BACKGROUND: The pathogenesis and treatment of colorectal cancer (CRC) continue to be areas of ongoing research, especially the benefits of traditional Chinese medicine (TCM) in slowing the progression of CRC. This study was conducted to investigate the effectiveness and mechanism of action of modified Lichong decoction (MLCD) in inhibiting CRC progression.

METHODS: We established CRC animal models using azoxymethane/dextran sodium sulfate (AOM/DSS) and administered high, medium, or low doses of MLCD or mesalazine (MS) for 9 weeks to observe MLCD alleviation of CRC. The optimal MLCD dose group was then subjected to metagenomic and RNA sequencing (RNA-seq) to explore the differentially abundant flora and genes in the control, model and MLCD groups. Finally, the mechanism of action was verified using WB, qRT‒PCR, immunohistochemistry and TUNEL staining.

RESULTS: MLCD inhibited the progression of CRC, and the optimal effect was observed at high doses. MLCD regulated the structure and function of the intestinal flora by decreasing the abundance of harmful bacteria and increasing that of beneficial bacteria. The differentially expressed genes were mainly associated with the Wnt/β-catenin pathway and the cell cycle. Molecular biology analysis indicated that MLCD suppressed the Wnt/β-catenin pathway and the epithelial-mesenchymal transition (EMT), inhibited abnormal cell proliferation and promoted intestinal epithelial cell apoptosis.

CONCLUSION: MLCD mitigated the abnormal growth of intestinal epithelial cells and promoted apoptosis, thereby inhibiting the progression of CRC. This inhibition was accomplished by modifying the intestinal microbiota and disrupting the Wnt/β-catenin pathway and the EMT. Therefore, MLCD could serve as a potential component of TCM prescriptions for CRC treatment.},
}

*Wnt Signaling Pathway/drug effects
*Gastrointestinal Microbiome/drug effects
Animals
*Colorectal Neoplasms/drug therapy/pathology/metabolism
*Drugs, Chinese Herbal/pharmacology
Mice
Humans
Male
Apoptosis/drug effects
Epithelial-Mesenchymal Transition/drug effects
Cell Proliferation/drug effects
Dextran Sulfate
beta Catenin/metabolism
Disease Models, Animal

@article {pmid38710672,
year = {2024},
author = {Ijoma, GN and Ogola, HJO and Pillay, P and Tshisekedi, KA and Tekere, M},
title = {Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {456},
pmid = {38710672},
issn = {2052-4463},
mesh = {*Lakes/microbiology ; *Eutrophication ; *Geologic Sediments/microbiology ; South Africa ; *Metagenomics ; *Metagenome ; Bacteria/genetics/classification ; Phylogeny ; Water Microbiology ; },
abstract = {We present metagenomes of 16 samples of water and sediment from two lakes, collected from eutrophic and non-eutrophic areas, including pooled samples enriched with phosphate and nitrate. Additionally, we assembled 167 bacterial metagenome-assembled genomes (MAGs). These MAGs were de-replicated into 83 unique genomes representing different species found in the lakes. All the MAGs exhibited >70% completeness and <10% contamination, with 79 MAGs being classified as 'nearly complete' (completeness >90%), while 54 falling within 80-90% range and 34 between 75-80% complete. The most abundant MAGs identified across all samples were Proteobacteria (n = 80), Firmicutes_A (n = 35), Firmicutes (n = 13), and Bacteriodota (n = 22). Other groups included Desulfobacteria_I (n = 2), Verrucomicrobiota (n = 4), Campylobacterota (n = 4) and Actinobacteriota (n = 6). Importantly, phylogenomic analysis identified that approximately 50.3% of the MAGs could not be classified to known species, suggesting the presence of potentially new and unknown bacteria in these lakes, warranting further in-depth investigation. This study provides valuable new dataset on the diverse and often unique microbial communities living in polluted lakes, useful in developing effective strategies to manage pollution.},
}

*Lakes/microbiology
*Eutrophication
*Geologic Sediments/microbiology
South Africa
*Metagenomics
*Metagenome
Bacteria/genetics/classification
Phylogeny
Water Microbiology

@article {pmid38710585,
year = {2024},
author = {Lu, Y and Li, S and Su, Z and Luo, C and Gu, M and Yuan, D and Qin, BE and Dai, K and Xia, H and Chen, Y and Peng, F and Jiang, Y},
title = {Presence of Epstein-Barr virus in cerebrospinal fluid is associated with increased mortality in HIV-negative cryptococcal meningitis.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myae052},
pmid = {38710585},
issn = {1460-2709},
abstract = {Cryptococcus neoformans is the most common cause of fungal meningitis and is associated with a high mortality. The clinical significance of concurrent Epstein-Barr virus (EBV) in the cerebrospinal fluid (CSF) of human immunodeficiency virus (HIV)-negative patients with cryptococcal meningitis (CM) remains unclear. A retrospective cohort study was performed by analyzing CSF samples from 79 HIV-negative Chinese Han patients with confirmed CM. We identified CSF viral DNA in these patients by metagenomic next-generation sequencing (mNGS) and compared 10-week survival rates among those with and without EBV DNA in CSF. Of 79 CSF samples tested, 44.3% (35/79) had detectable viral DNA in CSF, while 55.7% (44/79) were virus-negative. The most frequent viral pathogen was EBV, which was detected in 22.8% (18/79) patients. The median number of CSF-EBV DNA reads was 4 reads with a range from 1 to 149 reads. The 10-week mortality were 22.2% (4/18) in those with positive-CSF-EBV and 2.3% (1/44) in those with negative-CSF-virus (hazard ratio 8.20, 95% confidence interval [CI] 1.52-81.80; p=0.014), which remained significant after a multivariate adjustment for the known risk factors of mortality (adjusted hazard ratio 8.15, 95% CI 1.14-92.87; p=0.037). mNGS can identify viruses that coexist in CSF of HIV-negative patients with CM. EBV DNA is most commonly found together with Cryptococcus neoformans in CSF and its presence is associated with increased mortality in HIV-negative CM patients.},
}

@article {pmid38710431,
year = {2024},
author = {Zhu, Y and Li, R and Yan, S and Chen, X and Cen, S and Xie, S},
title = {Habitat- and lifestyle-dependent structural and functional characteristics of viruses in mangrove wetlands of different functional zonings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119070},
doi = {10.1016/j.envres.2024.119070},
pmid = {38710431},
issn = {1096-0953},
abstract = {Mangrove wetlands, as one of the natural ecosystems with the most ecological services, have garnered widespread attention about their microbial driven biogeochemical cycling. Urbanization have led to different spatial patterns of environmental conditions and microbial communities in mangroves. However, viruses, as the pivotal drivers of biogeochemical cycling in mangroves, remain inadequately explored in terms of how their ecological potential and complex interactions with host respond to functional zonings. To address this knowledge gap, we conducted a comprehensive investigation on the structural and functional properties of temperate and lytic viruses in mangrove wetlands from different functional zonings by jointly using high-throughput sequencing, prokaryotic and viral metagenomics. Multiple environmental factors were found to significantly influence the taxonomic and functional composition, as well as lysogen-lysis decision-making of mangrove viruses. Furthermore, enriched auxiliary metabolic genes (AMGs) involved in methane, nitrogen and sulfur metabolism, and heavy metal resistance were unveiled in mangrove viruses, whose community composition was closely related to lifestyle and host. The virus-host pairs with different lifestyles were also discovered to react to environmental changes in different ways, which provided an empirical evidence for how virus and bacteria dynamics were specific to viral lifestyles in nature. This study expands our comprehension of the intricate interactions among virus, prokaryotic host and the environment in mangrove wetlands from multiple perspectives, including viral lifestyles, virus-host interactions, and habitat dependence. Importantly, it provides a new ecological perspective on how mangrove viruses are adapted to the stress posed by urbanization.},
}

@article {pmid38709876,
year = {2024},
author = {Zhao, J and Nair, S and Zhang, Z and Wang, Z and Jiao, N and Zhang, Y},
title = {Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae083},
pmid = {38709876},
issn = {1751-7370},
abstract = {The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g., deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g., laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.},
}

@article {pmid38709734,
year = {2024},
author = {Yahara, H and Yanamoto, S and Takahashi, M and Hamada, Y and Asaka, T and Kitagawa, Y and Moridera, K and Noguchi, K and Maruoka, Y and Yahara, K},
title = {Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0302569},
doi = {10.1371/journal.pone.0302569},
pmid = {38709734},
issn = {1932-6203},
mesh = {Humans ; *Saliva/microbiology ; *Osteomyelitis/microbiology ; Female ; *Microbiota/genetics ; Male ; Middle Aged ; *Metagenomics/methods ; Chronic Disease ; Adult ; Metagenome ; Aged ; },
abstract = {Osteomyelitis of the jaw is a severe inflammatory disorder that affects bones, and it is categorized into two main types: chronic bacterial and nonbacterial osteomyelitis. Although previous studies have investigated the association between these diseases and the oral microbiome, the specific taxa associated with each disease remain unknown. In this study, we conducted shotgun metagenome sequencing (≥10 Gb from ≥66,395,670 reads per sample) of bulk DNA extracted from saliva obtained from patients with chronic bacterial osteomyelitis (N = 5) and chronic nonbacterial osteomyelitis (N = 10). We then compared the taxonomic composition of the metagenome in terms of both taxonomic and sequence abundances with that of healthy controls (N = 5). Taxonomic profiling revealed a statistically significant increase in both the taxonomic and sequence abundance of Mogibacterium in cases of chronic bacterial osteomyelitis; however, such enrichment was not observed in chronic nonbacterial osteomyelitis. We also compared a previously reported core saliva microbiome (59 genera) with our data and found that out of the 74 genera detected in this study, 47 (including Mogibacterium) were not included in the previous meta-analysis. Additionally, we analyzed a core-genome tree of Mogibacterium from chronic bacterial osteomyelitis and healthy control samples along with a reference complete genome and found that Mogibacterium from both groups was indistinguishable at the core-genome and pan-genome levels. Although limited by the small sample size, our study provides novel evidence of a significant increase in Mogibacterium abundance in the chronic bacterial osteomyelitis group. Moreover, our study presents a comparative analysis of the taxonomic and sequence abundances of all genera detected using deep salivary shotgun metagenome data. The distinct enrichment of Mogibacterium suggests its potential as a marker to distinguish between patients with chronic nonbacterial osteomyelitis and chronic bacterial osteomyelitis, particularly at the early stages when differences are unclear.},
}

Humans
*Saliva/microbiology
*Osteomyelitis/microbiology
Female
*Microbiota/genetics
Male
Middle Aged
*Metagenomics/methods
Chronic Disease
Adult
Metagenome
Aged

@article {pmid38709343,
year = {2024},
author = {Halema, AA and El-Beltagi, HS and Al-Dossary, O and Alsubaie, B and Henawy, AR and Rezk, AA and Almutairi, HH and Mohamed, AA and Elarabi, NI and Abdelhadi, AA},
title = {Omics technology draws a comprehensive heavy metal resistance strategy in bacteria.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {6},
pages = {193},
pmid = {38709343},
issn = {1573-0972},
support = {5872//Deanship of Scientific Research, Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Saudi Arabia/ ; },
mesh = {*Metals, Heavy/metabolism ; *Bacteria/genetics/metabolism/drug effects ; *Biodegradation, Environmental ; Genome, Bacterial ; Proteomics ; Transcriptome ; Metagenomics ; Metagenome ; Genomics ; Drug Resistance, Bacterial/genetics ; },
abstract = {The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.},
}

*Metals, Heavy/metabolism
*Bacteria/genetics/metabolism/drug effects
*Biodegradation, Environmental
Genome, Bacterial
Proteomics
Transcriptome
Metagenomics
Metagenome
Genomics
Drug Resistance, Bacterial/genetics

@article {pmid38709303,
year = {2024},
author = {Veschetti, L and Paiella, S and Carelli, M and Zotti, F and Secchettin, E and Malleo, G and Signoretto, C and Zulianello, G and Nocini, R and Crovetto, A and Salvia, R and Bassi, C and Malerba, G},
title = {Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {319},
pmid = {38709303},
issn = {1432-0614},
mesh = {Humans ; *Metagenomics/methods ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Drug Resistance, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.},
}

Humans
*Metagenomics/methods
*Dental Plaque/microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Drug Resistance, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenome

@article {pmid38709227,
year = {2024},
author = {Unzueta-Medina, JA and González-Chávez, SA and Salas-Leiva, JS and Silva-Sánchez, SE and Pacheco-Tena, C},
title = {Differential Composition and Structure of the Microbiota from Active and Inactive Stages of HLA-B27-associated Uveitis by Paired Fecal Metagenomes.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/09273948.2024.2346818},
pmid = {38709227},
issn = {1744-5078},
abstract = {PURPOSE: To compare the diversities and abundances of bacterial taxa in the microbiome of patients with HLA B27-positive acute anterior uveitis (AAU) in the active and inactive phases.

METHODS: An observational descriptive prospective and comparative study was conducted in ten HLA-B27-positive AAU patients (44.6 ± 13.4 years). The microbiome of the stool samples obtained in the active and inactive stages was analyzed by sequencing the V3 region of the 16S rRNA gene.

RESULTS: The differences in the bacteria profile between active and inactive stages in each individual were confirmed (p < 0.0001). Ten OTUs were found exclusively in the active phase of 90% of the individuals, suggesting a proinflammatory association. Blautia OUT_4 and Faecalibacterium OUT_2 abundances showed a direct relationship between abundance and severity of ocular inflammation. Two OTUs were exclusive of the inactive stage, suggesting an anti-inflammatory role.

CONCLUSION: The metagenomic profile of the fecal microbiota differs in the acute phase of the AAU compared to when the inflammation subsides, despite being the same individual and a short time-lapse. AAU is a fertile field for studying the connection between subtle rapid changes in microbiota and their systemic consequences.},
}

@article {pmid38709214,
year = {2024},
author = {Li, Y and Wang, T and Jing, H and Xiao, Y},
title = {Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep-sea biosphere.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17372},
doi = {10.1111/mec.17372},
pmid = {38709214},
issn = {1365-294X},
abstract = {The NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophic pathway. Although numerous amplicon-based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep-sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep-sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome-assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite-dependent anaerobic methane oxidation (n-DAMO) occurs within deep-sea sediments. In addition, the identification of the Wood-Ljungdahl (WL) and 3-hydroxypropionate/4-hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep-sea environments. Indeed, we found that for their survival in the oligotrophic deep-sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl-CoA from the carbonyl branch for citric acid cycle-based energy production and methane from the methyl branch for n-DAMO. The observed low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS) in n-DAMO-related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep-sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep-sea ecosystems, driven by this bacterial phylum.},
}

@article {pmid38708959,
year = {2024},
author = {Kousgaard, SJ and Cold, F and Halkjær, SI and Petersen, AM and Kjeldsen, J and Møller Hansen, J and Dall, SM and Albertsen, M and Nielsen, HL and Kirk, KF and Duch, K and Sønderkær, M and Thorlacius-Ussing, O},
title = {The effect of non-pooled multi-donor faecal microbiota transplantation for inducing clinical remission in patients with chronic pouchitis: Results from a multicentre randomised double-blinded placebo-controlled trial (MicroPouch).},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjae066},
pmid = {38708959},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: To investigate if treatment with non-pooled multi-donor faecal microbiota transplantation (FMT) for four weeks was superior to placebo to induce clinical remission in patients with chronic pouchitis.

METHODS: The study was a randomised double-blinded placebo-controlled study with a 4-week intervention period and 12-month follow-up. Eligible patients with chronic pouchitis were recruited from five Danish hospitals. Participants were randomised to non-pooled multi-donor FMT derived from four faecal donors, or placebo. Treatment was delivered daily by enema for two weeks followed by every second day for two weeks. Disease severity was accessed at inclusion and 30-day follow-up, using the Pouchitis Disease Activity Index (PDAI); PDAI <7 was considered equivalent to clinical remission. Faecal samples from participants and donors were analysed by shotgun metagenomic sequencing.

RESULTS: Inclusion was stopped after inclusion of 30 participants who were randomised 1:1 for treatment with FMT or placebo. There was no difference in participants achieving clinical remission between the two groups at 30-day follow-up, relative risk 1.0 (95%CI(0.55;1.81)). Treatment with FMT resulted in a clinically relevant increase in adverse events compared to placebo, incidence rate ratio 1.67 (95%CI(1.10;2.52)); no serious adverse events within either group. Faecal microbiota transplantation statistically significantly increased the similarity of participant faecal microbiome to the faecal donor microbiome at 30-days follow-up (p=0.01), which was not seen after placebo.

CONCLUSIONS: Non-pooled multi-donor FMT was comparable to placebo in inducing clinical remission in patients with chronic pouchitis but showed a clinically relevant increase in adverse events compared to placebo.},
}

@article {pmid38708883,
year = {2024},
author = {El Mouzan, M and Al Mofarreh, M and Alsaleem, B and Al Sarkhy, A and Alanazi, A and Khormi, M and Almasoud, A and Assiri, A},
title = {Bacterial dysbiosis in newly diagnosed treatment naïve pediatric ulcerative colitis in Saudi Arabia.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
doi = {10.4103/sjg.sjg_66_24},
pmid = {38708883},
issn = {1998-4049},
abstract = {BACKGROUND: The role of microbiota in the pathogenesis of ulcerative colitis (UC) has been increasingly recognized. However, most of the reports are from Western populations. In Middle Eastern countries, including Saudi Arabia, little is known about the role of microbiota. Therefore, our aim was to describe the bacterial microbiota profile and signature in pediatric UC in Saudi Arabia.

METHODS: Twenty children with UC and 20 healthy controls enrolled in the study gave stool samples. Twenty rectal mucosal samples were taken from UC and 20 from non-UC controls. Inclusion criteria included newly diagnosed and untreated children and lack of antibiotic exposure for at least 6 months before stool collection was required for children with UC and controls. Bacterial deoxyribonucleic acid was extracted and sequenced using shotgun metagenomic analysis. Statistical analysis included Shannon alpha diversity metrics, Bray-Curtis dissimilarity, DESeq2, and biomarker discovery.

RESULTS: The demographic characteristics were similar in children with UC and controls. There was a significant reduction in alpha diversity (P = 0.037) and beta diversity in samples from children with UC (P = 0.001). Many taxa were identified with log2 abundance analysis, revealing 110 and 102 species significantly depleted and enriched in UC, respectively. Eleven bacterial species' signatures were identified.

CONCLUSIONS: In Saudi Arabian children with UC, we demonstrate a dysbiosis similar to reports from Western populations, possibly related to changes of lifestyle. Microbial signature discovery in this report is an important contribution to research, leading to the development of adjunctive non-invasive diagnostic options in unusual cases of UC.},
}

@article {pmid38708423,
year = {2024},
author = {Yamaguchi, M and Uchihashi, T and Kawabata, S},
title = {Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution.},
journal = {Biochemistry and biophysics reports},
volume = {38},
number = {},
pages = {101717},
pmid = {38708423},
issn = {2405-5808},
abstract = {Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.},
}

@article {pmid38707986,
year = {2024},
author = {Qi, Q and Yang, J and Yang, L and Tian, H and Wan, C and Liu, D},
title = {Diagnostic and Therapeutic Challenges in Lemierre Syndrome: A Case Report Using Metagenomic Next Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1669-1673},
pmid = {38707986},
issn = {1178-6973},
abstract = {Lemierre syndrome (LS) is a rare and life-threatening condition predominantly caused by Fusobacterium necrophorum. Currently, there are no standardized clinical guidelines for LS management. Here, we describe the case of a 40-year-old male with fever, productive cough, and dyspnea but no sore throat. Diagnostic radiological examinations revealed multiple pulmonary cavitary nodules and an internal jugular vein occlusion. Metagenomic Next-Generation Sequencing (mNGS) of the alveolar lavage fluid identified Fusobacterium necrophorum, thereby confirming the diagnosis of LS. Intriguingly, the patient exhibited a delayed clinical response despite receiving the appropriate antibiotic. After integrating tigecycline into the treatment to address potential co-infecting bacteria, we observed a marked improvement in his clinical symptoms. Subsequent follow-up over 12 weeks post-discharge revealed complete alleviation of symptoms, and a chest CT scan showed marked regression of the lung lesions.},
}

@article {pmid38707845,
year = {2024},
author = {Rivas-Santisteban, J and Yubero, P and Robaina-Estévez, S and González, JM and Tamames, J and Pedrós-Alió, C},
title = {Quantifying microbial guilds.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae042},
pmid = {38707845},
issn = {2730-6151},
abstract = {The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.},
}

@article {pmid38707840,
year = {2024},
author = {Maire, J and Collingro, A and Horn, M and van Oppen, MJH},
title = {Chlamydiae in corals: shared functional potential despite broad taxonomic diversity.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae054},
pmid = {38707840},
issn = {2730-6151},
abstract = {Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.},
}

@article {pmid38707513,
year = {2024},
author = {Kuenzli, AB and Müller, MD and Z Graggen, WJ and Walti, LN and Martin, Y and Lazarevic, V and Schrenzel, J and Oberli, A},
title = {Case report: Chronic Candida albicans meningitis: a rare entity diagnosed by metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1322847},
pmid = {38707513},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; Adult ; *Candida albicans/genetics/isolation & purification ; *Meningitis, Fungal/diagnosis/microbiology/drug therapy ; *Metagenomics/methods ; Candidiasis/diagnosis/microbiology/cerebrospinal fluid ; Male ; Chronic Disease ; Antifungal Agents/therapeutic use ; Meningitis, Aseptic/diagnosis ; },
abstract = {The aetiology of chronic aseptic meningitis is difficult to establish. Candida meningitis in particular is often diagnosed late, as cerebrospinal fluid (CSF) work-up and imaging findings are nonspecific. A 35-year-old patient with chronic aseptic meningitis, for which repeated microbiological testing of CSF was unrevealing, was finally diagnosed with Candida albicans (C. albicans) meningitis with cauda equina involvement using metagenomic next-generation sequencing (mNGS). This report highlights the diagnostic challenges and the difficulties of treating shunt-associated fungal meningitis.},
}

Humans
*High-Throughput Nucleotide Sequencing
Adult
*Candida albicans/genetics/isolation & purification
*Meningitis, Fungal/diagnosis/microbiology/drug therapy
*Metagenomics/methods
Candidiasis/diagnosis/microbiology/cerebrospinal fluid
Male
Chronic Disease
Antifungal Agents/therapeutic use
Meningitis, Aseptic/diagnosis

@article {pmid38706006,
year = {2024},
author = {Liew, KJ and Shahar, S and Shamsir, MS and Shaharuddin, NB and Liang, CH and Chan, KG and Pointing, SB and Sani, RK and Goh, KM},
title = {Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {29},
pmid = {38706006},
issn = {2524-6372},
support = {FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; 4J549//UTM QuickWin grant/ ; 4J549//UTM QuickWin grant/ ; T2EP30123-0028//Singapore Ministry of Education ARC Tier 2 fund/ ; 1736255, 1849206, and 1920954//National Science Foundation/ ; },
abstract = {BACKGROUND: Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.

RESULTS: Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.

CONCLUSIONS: This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.},
}

@article {pmid38705650,
year = {2024},
author = {Powell, AM and Ali Khan, FZ and Ravel, J and Elovitz, MA},
title = {Untangling Associations of Microbiomes of Pregnancy and Preterm Birth.},
journal = {Clinics in perinatology},
volume = {51},
number = {2},
pages = {425-439},
pmid = {38705650},
issn = {1557-9840},
mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/microbiology/epidemiology ; *Vagina/microbiology ; *Microbiota ; Infant, Newborn ; *Placenta/microbiology ; *Gastrointestinal Microbiome/physiology ; Lactobacillus ; Mouth/microbiology ; },
abstract = {This review illuminates the complex interplay between various maternal microbiomes and their influence on preterm birth (PTB), a driving and persistent contributor to neonatal morbidity and mortality. Here, we examine the dynamics of oral, gastrointestinal (gut), placental, and vaginal microbiomes, dissecting their roles in the pathogenesis of PTB. Importantly, focusing on the vaginal microbiome and PTB, the review highlights (1) a protective role of Lactobacillus species; (2) an increased risk with select anaerobes; and (3) the influence of social health determinants on the composition of vaginal microbial communities.},
}

Humans
Female
Pregnancy
*Premature Birth/microbiology/epidemiology
*Vagina/microbiology
*Microbiota
Infant, Newborn
*Placenta/microbiology
*Gastrointestinal Microbiome/physiology
Lactobacillus
Mouth/microbiology

@article {pmid38705450,
year = {2024},
author = {Zhang, Y and Wang, M and Zhou, X and Cheng, W and Ren, J and Wan, T and Liu, X},
title = {Transmission mechanism of antibiotic resistance genes and their differences between water and sediment in the Weihe River Basin.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119057},
doi = {10.1016/j.envres.2024.119057},
pmid = {38705450},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) are emerging microbial pollutants that are regulated by many factors and pose potential threats to aquatic environments. In this study, we used network analysis, correlation analysis, and constructed models based on metagenomic sequencing results to explore the spatial patterns, impact mechanisms, transmission risks and differences in ARGs in the water and sediment of the Weihe River Basin. The findings revealed notable disparities in ARGs, mobile genetic elements (MGEs), and bacterial communities. In the sediment, the abundance of ARGs was considerably greater than that in water. Moreover, the percentage of ARGs shared by the two components reached a value of 85.8%. Through network analysis, it was determined that the presence of 16 MGEs and 20 bacterial phyla was strongly associated with ARGs (R[2]>0.7, P<0.05). The Mantel test showed that abiotic factors including DO, pH, nutrients, and heavy metals played important roles in the distribution of ARGs (P<0.05). A structural equation model revealed that the key factors influencing the distribution of ARGs in water were bacterial diversity and environmental parameters (standardized effects of -0.730 and -0.667), and those in sediment were bacterial diversity and MGEs (standardized effects of -0.751 and 0.851). Neutral modeling indicated that deterministic processes played an important role in the assembly of ARGs in the water of the Weihe River Basin, and stochastic processes were dominant in the sediment. There was a highly significant positive linear correlation between ARGs and pathogens, and there was more complex co-occurrence in the water than in the sediment (R[2]>0.9, P<0.05), with stronger migration and transmission occurring. Exploring ARGs in large-scale watersheds is immensely important for elucidating their traits and transmission mechanisms and consequently paving the way for the formulation of efficient strategies to mitigate resistance threats.},
}

@article {pmid38705355,
year = {2024},
author = {Schäfer, L and Jehle, JA and Kleespies, RG and Wennmann, JT},
title = {Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108121},
doi = {10.1016/j.jip.2024.108121},
pmid = {38705355},
issn = {1096-0805},
abstract = {The oak processionary moth (OPM) Thaumetopoea processionea is a pest of oak trees and poses health risks to humans due to the urticating setae of later instar larvae. For this reason, it is difficult to rear OPM under laboratory conditions, carry out bioassays or examine larvae for pathogens. Biological control targets the early larval instars and is based primarily on commercial preparations of Bacillus thuringiensis ssp. kurstaki (Btk). To test the entomopathogenic potential of other spore-forming bacteria, a user-friendly bioassay system was developed that (i) applies bacterial spore suspensions by oak bud dipping, (ii) targets first larval instar larvae through feeding exposure and (iii) takes into account their group-feeding behavior. A negligible mortality in the untreated control proved the functionality of the newly established bioassay system. Whereas the commercial Btk HD-1 strain was used as a bioassay standard and confirmed as being highly efficient, a B. wiedmannii strain was ineffective in killing OPM larvae. Larvae, which died during the infection experiment, were further subjected to Nanopore sequencing for a metagenomic approach for entomopathogen detection. It further corroborated that B.wiedmannii was not able to infect and establish in OPM, but identified potential insect pathogenic species from the genera Serratia and Pseudomonas.},
}

@article {pmid38705068,
year = {2024},
author = {Shao, B and Niu, L and Xie, YG and Zhang, R and Wang, W and Xu, X and Sun, J and Xing, D and Lee, DJ and Ren, N and Hua, ZS and Chen, C},
title = {Overlooked in-situ sulfur disproportionation fuels dissimilatory nitrate reduction to ammonium in sulfur-based system: Novel insight of nitrogen recovery.},
journal = {Water research},
volume = {257},
number = {},
pages = {121700},
doi = {10.1016/j.watres.2024.121700},
pmid = {38705068},
issn = {1879-2448},
abstract = {Sulfur-based denitrification is a promising technology in treatments of nitrate-contaminated wastewaters. However, due to weak bioavailability and electron-donating capability of elemental sulfur, its sulfur-to-nitrate ratio has long been low, limiting the support for dissimilatory nitrate reduction to ammonium (DNRA) process. Using a long-term sulfur-packed reactor, we demonstrate here for the first time that DNRA in sulfur-based system is not negligible, but rather contributes a remarkable 40.5 %-61.1 % of the total nitrate biotransformation for ammonium production. Through combination of kinetic experiments, electron flow analysis, 16S rRNA amplicon, and microbial network succession, we unveil a cryptic in-situ sulfur disproportionation (SDP) process which significantly facilitates DNRA via enhancing mass transfer and multiplying 86.7-210.9 % of bioavailable electrons. Metagenome assembly and single-copy gene phylogenetic analysis elucidate the abundant genomes, including uc_VadinHA17, PHOS-HE36, JALNZU01, Thiobacillus, and Rubrivivax, harboring complete genes for ammonification. Notably, a unique group of self-SDP-coupled DNRA microorganism was identified. This study unravels a previously concealed fate of DNRA, which highlights the tremendous potential for ammonium recovery and greenhouse gas mitigation. Discovery of a new coupling between nitrogen and sulfur cycles underscores great revision needs of sulfur-driven denitrification technology.},
}

@article {pmid38705065,
year = {2024},
author = {Pan, J and Li, J and Zhang, T and Liu, T and Xu, K and Wang, C and Zheng, M},
title = {Complete ammonia oxidation (comammox) at pH 3-4 supports stable production of ammonium nitrate from urine.},
journal = {Water research},
volume = {257},
number = {},
pages = {121686},
doi = {10.1016/j.watres.2024.121686},
pmid = {38705065},
issn = {1879-2448},
abstract = {This study developed a new process that stably produced ammonium nitrate (NH4NO3), an important and commonly used fertilizer, from the source-separated urine by comammox Nitrospira. In the first stage, the complete conversion of ammonium to nitrate was achieved by comammox Nitrospira. In this scenario, the pH was maintained at 6 by adding external alkali, which also provided sufficient alkalinity for full nitrification. In the second stage, the NH4NO3 was produced directly by comammox Nitropsira by converting half of the ammonium in urine into nitrate. In this case, no alkali was added and pH automatically dropped and self-maintained at an extremely acidic level (pH 3-4). In both scenarios, negligible nitrite accumulation was observed, while the final product of the second stage contained ammonium and nitrate at the molar ratio of 1:1. The dominance of comammox Nitrospira over canonical ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was systematically proved by the combination of 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction, and metagenomics. Notably, metagenomic sequencing suggested that the relative abundance of comammox Nitrospira was over 20 % under the acidic condition at pH 3-4, while canonical AOB and NOB were undetectable. Batch experiments showed that the optimal pH for the enriched comammox Nitrospira was ∼7, which could sustain their activity in a wider pH range from 4 to 8 surprisingly but lost activity at pH 3 and 9. The findings not only present an application potential of comammox Nitrospira in nitrogen recovery from urine wastewater but also report the survivability of comammox bacteria in acidic environments.},
}

@article {pmid38704474,
year = {2024},
author = {Eltokhy, MA and Saad, BT and Eltayeb, WN and Alshahrani, MY and Radwan, SMR and Aboshanab, KM and Ashour, MSE},
title = {Metagenomic nanopore sequencing for exploring the nature of antimicrobial metabolites of Bacillus haynesii.},
journal = {AMB Express},
volume = {14},
number = {1},
pages = {52},
pmid = {38704474},
issn = {2191-0855},
abstract = {Multidrug-resistant (MDR) pathogens are a rising global health worry that imposes an urgent need for the discovery of novel antibiotics particularly those of natural origin. In this context, we aimed to use the metagenomic nanopore sequence analysis of soil microbiota coupled with the conventional phenotypic screening and genomic analysis for identifying the antimicrobial metabolites produced by promising soil isolate(s). In this study, whole metagenome analysis of the soil sample(s) was performed using MinION™ (Oxford Nanopore Technologies). Aligning and analysis of sequences for probable secondary metabolite gene clusters were extracted and analyzed using the antiSMASH version 2 and DeepBGC. Results of the metagenomic analysis showed the most abundant taxa were Bifidobacterium, Burkholderia, and Nocardiaceae (99.21%, followed by Sphingomonadaceae (82.03%) and B. haynesii (34%). Phenotypic screening of the respective soil samples has resulted in a promising Bacillus isolate that exhibited broad-spectrum antibacterial activities against various MDR pathogens. It was identified using microscopical, cultural, and molecular methods as Bacillus (B.) haynesii isolate MZ922052. The secondary metabolite gene analysis revealed the conservation of seven biosynthetic gene clusters of antibacterial metabolites namely, siderophore lichenicidin VK21-A1/A2 (95% identity), lichenysin (100%), fengycin (53%), terpenes (100%), bacteriocin (100%), Lasso peptide (95%) and bacillibactin (53%). In conclusion, metagenomic nanopore sequence analysis of soil samples coupled with conventional screening helped identify B. haynesii isolate MZ922052 harboring seven biosynthetic gene clusters of promising antimicrobial metabolites. This is the first report for identifying the bacteriocin, lichenysin, and fengycin biosynthetic gene clusters in B. haynesii MZ922052.},
}

@article {pmid38704005,
year = {2024},
author = {Lv, B and Jiang, C and Han, Y and Wu, D and Jin, L and Zhu, G and An, T and Shi, J},
title = {Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119056},
doi = {10.1016/j.envres.2024.119056},
pmid = {38704005},
issn = {1096-0953},
abstract = {Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.},
}

@article {pmid38703955,
year = {2024},
author = {Wei, CH and Wang, ZW and Dai, JH and Xiao, K and Yu, HR and Qu, FS and Rong, HW and He, JG and Hao Ngo, H},
title = {Enhanced anaerobic digestion performance and sludge filterability by membrane microaeration for anaerobic membrane bioreactor application.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130787},
doi = {10.1016/j.biortech.2024.130787},
pmid = {38703955},
issn = {1873-2976},
abstract = {Slow dissolution/hydrolysis of insoluble/macromolecular organics and poor sludge filterability restrict the application potential of anaerobic membrane bioreactor (AnMBR). Bubble-free membrane microaeration was firstly proposed to overcome these obstacles in this study. The batch anaerobic digestion tests feeding insoluble starch and soluble peptone with and without microaeration showed that microaeration led to a 65.7-144.8% increase in methane production and increased critical flux of microfiltration membrane via driving the formation of large sludge flocs and the resultant improvement of sludge settleability. The metagenomic and bioinformatic analyses showed that microaeration significantly enriched the functional genes and bacteria for polysaccharide and protein hydrolysis, microaeration showed little negative effects on the functional genes involved in anaerobic metabolisms, and substrate transfer from starch to peptone significantly affected the functional genes and microbial community. This study demonstrates the dual synergism of microaeration to enhance the dissolution/hydrolysis/acidification of insoluble/macromolecular organics and sludge filterability for AnMBR application.},
}

@article {pmid38703845,
year = {2024},
author = {Han, B and He, Y and Chen, J and Wang, Y and Shi, L and Lin, Z and Yu, L and Wei, X and Zhang, W and Geng, Y and Shao, X and Jia, S},
title = {Different microbial functional traits drive bulk and rhizosphere soil phosphorus mobilization in an alpine meadow after nitrogen input.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172904},
doi = {10.1016/j.scitotenv.2024.172904},
pmid = {38703845},
issn = {1879-1026},
abstract = {Enhanced nitrogen (N) input is expected to influence the soil phosphorus (P) cycling through biotic and abiotic factors. Among these factors, soil microorganisms play a vital role in regulating soil P availability. However, the divergent contribution of functional microorganisms to soil P availability in the rhizosphere and bulk soil under N addition remains unclear. We conducted an N addition experiment with four N input rates (0, 5,10, and 15 g N m[-2] year[-1]) in an alpine meadow over three years. Metagenomics was employed to investigate the functional microbial traits in the rhizosphere and bulk soil. We showed that N addition had positive effects on microbial functional traits related to P-cycling in the bulk and rhizosphere soil. Specifically, high N addition significantly increased the abundance of most microbial genes in the bulk soil but only enhanced the abundance of five genes in the rhizosphere soil. The soil compartment, rather than the N addition treatment, was the dominant factor explaining the changes in the diversity and network of functional microorganisms. Furthermore, the abundance of functional microbial genes had a profound effect on soil available P, particularly in bulk soil P availability driven by the ppa and ppx genes, as well as rhizosphere soil P availability driven by the ugpE gene. Our results highlight that N addition stimulates the microbial potential for soil P mobilization in alpine meadows. Distinct microbial genes play vital roles in soil P availability in bulk and rhizosphere soil respectively. This indicates the necessity for models to further our knowledge of P mobilization processes from the bulk soil to the rhizosphere soil, allowing for more precise predictions of the effects of N enrichment on soil P cycling.},
}

@article {pmid38703812,
year = {2024},
author = {Manoharan-Basil, SS and Gestels, Z and Abdelatti, S and De Baetselier, I and Vanbaelen, T and Hinterwirth, A and Doan, T and Lietman, T and Kenyon, C},
title = {Could the effect of antimicrobials on antimicrobial resistance be saturated at high antimicrobial consumption? A comparison of the MORDOR and ResistAZM studies.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {107082},
doi = {10.1016/j.ijid.2024.107082},
pmid = {38703812},
issn = {1878-3511},
abstract = {BACKGROUND AND OBJECTIVES: Antimicrobial resistance poses a considerable threat in high-antimicrobial-consumption populations, such as men who have sex with men (MSM) taking HIV pre-exposure prophylaxis. While the ResistAZM trial found no increase in macrolide resistance genes in MSM with gonorrhea after azithromycin treatment, the MORDOR trial observed an increase in these genes after mass azithromycin distribution. We hypothesized that this could be due to saturation of the resistome. To test this hypothesis, we compared the abundance of macrolide resistance determinants in anorectal samples between the baselines of the two trials.

METHODS: Shotgun metagenome reads from the anorectal baseline samples from the ResistAZM (n=42) and MORDOR (n=30) trials were analyzed using AMRPlusPlus. Non-host reads were mapped to the MEGARes database to detect antibiotic resistance genes (ARG). AMR was normalized using cumulative sum scaling, and ARG abundance was estimated.

RESULTS: Macrolide, lincosamides and streptogramins (MLS) determinants were approximately 10-fold more abundant in the ResistAZM than the MORDOR samples (p = <0.001).

CONCLUSIONS: The findings are compatible with our hypothesis. Thus, in populations with high antimicrobial use, the relationship between antimicrobial consumption and AMR may be diminished due to saturation. These findings are vital for future studies investigating the resistogencity of novel interventions, such as doxycycline post-exposure prophylaxis, in populations with high preceding consumption of antimicrobials.},
}

@article {pmid38703502,
year = {2024},
author = {Kandathil, AJ and Thomas, DL},
title = {The Blood Virome: A new frontier in biomedical science.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {175},
number = {},
pages = {116608},
doi = {10.1016/j.biopha.2024.116608},
pmid = {38703502},
issn = {1950-6007},
abstract = {Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.},
}

@article {pmid38703419,
year = {2024},
author = {St John, E and Reysenbach, AL},
title = {Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {2-3},
pages = {126507},
doi = {10.1016/j.syapm.2024.126507},
pmid = {38703419},
issn = {1618-0984},
abstract = {Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse Thermoproteota. Despite their prevalence in high-temperature submarine communities, Thermoproteota are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the Aeropyrum-Thermodiscus-Caldisphaera. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the Aeropyrum-Thermodiscus-Caldisphaera. At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. Tiamatella incendiivivens, Hestiella acidicharens and Calypsonella navitae. A fourth genus was also identified related to Thermodiscus maritimus, for which no available sequenced genome exists. We propose the novel species Thermodiscus eudorianus to describe our high-quality Thermodiscus MAG, which represents the type genome for the genus. All three novel genera and T. eudorianus are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some Tiamatella, Calypsonella and T. eudorianus may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, Hestiella, may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family Acidilobaceae be amended to include Caldisphaera, Aeropyrum, Thermodiscus and Stetteria and the novel genera described here.},
}

@article {pmid38702804,
year = {2024},
author = {Das, R and Mishra, P and Mishra, B and Jha, R},
title = {Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens.},
journal = {Journal of animal science and biotechnology},
volume = {15},
number = {1},
pages = {62},
pmid = {38702804},
issn = {1674-9782},
abstract = {BACKGROUND: Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17[th] embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.

RESULTS: The results were considered significantly different at P < 0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21.

CONCLUSION: In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.},
}

@article {pmid38702796,
year = {2024},
author = {Morsli, M and Salipante, F and Magnan, C and Dunyach-Remy, C and Sotto, A and Lavigne, JP},
title = {Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {39},
pmid = {38702796},
issn = {1476-0711},
mesh = {Humans ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification ; *High-Throughput Nucleotide Sequencing ; Wound Healing ; Microbiota/genetics ; Pressure Ulcer/microbiology ; Diabetic Foot/microbiology ; Wound Infection/microbiology ; Varicose Ulcer/microbiology ; },
abstract = {BACKGROUND: Non-surgical chronic wounds, including diabetes-related foot diseases (DRFD), pressure injuries (PIs) and venous leg ulcers (VLU), are common hard-to-heal wounds. Wound evolution partly depends on microbial colonisation or infection, which is often confused by clinicians, thereby hampering proper management. Current routine microbiology investigation of these wounds is based on in vitro culture, focusing only on a limited panel of the most frequently isolated bacteria, leaving a large part of the wound microbiome undocumented.

METHODS: A literature search was conducted on original studies published through October 2022 reporting metagenomic next generation sequencing (mNGS) of chronic wound samples. Studies were eligible for inclusion if they applied 16 S rRNA metagenomics or shotgun metagenomics for microbiome analysis or diagnosis. Case reports, prospective, or retrospective studies were included. However, review articles, animal studies, in vitro model optimisation, benchmarking, treatment optimisation studies, and non-clinical studies were excluded. Articles were identified in PubMed, Google Scholar, Web of Science, Microsoft Academic, Crossref and Semantic Scholar databases.

RESULTS: Of the 3,202 articles found in the initial search, 2,336 articles were removed after deduplication and 834 articles following title and abstract screening. A further 14 were removed after full text reading, with 18 articles finally included. Data were provided for 3,628 patients, including 1,535 DRFDs, 956 VLUs, and 791 PIs, with 164 microbial genera and 116 species identified using mNGS approaches. A high microbial diversity was observed depending on the geographical location and wound evolution. Clinically infected wounds were the most diverse, possibly due to a widespread colonisation by pathogenic bacteria from body and environmental microbiota. mNGS data identified the presence of virus (EBV) and fungi (Candida and Aspergillus species), as well as Staphylococcus and Pseudomonas bacteriophages.

CONCLUSION: This study highlighted the benefit of mNGS for time-effective pathogen genome detection. Despite the majority of the included studies investigating only 16 S rDNA, ignoring a part of viral, fungal and parasite colonisation, mNGS detected a large number of bacteria through the included studies. Such technology could be implemented in routine microbiology for hard-to-heal wound microbiota investigation and post-treatment wound colonisation surveillance.},
}

Humans
*Metagenomics/methods
*Bacteria/genetics/isolation & purification/classification
*High-Throughput Nucleotide Sequencing
Wound Healing
Microbiota/genetics
Pressure Ulcer/microbiology
Diabetic Foot/microbiology
Wound Infection/microbiology
Varicose Ulcer/microbiology

@article {pmid38702766,
year = {2024},
author = {Guitart-Matas, J and Ballester, M and Fraile, L and Darwich, L and Giler-Baquerizo, N and Tarres, J and López-Soria, S and Ramayo-Caldas, Y and Migura-Garcia, L},
title = {Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {24},
pmid = {38702766},
issn = {2524-4671},
support = {RYC2019-027244-I//Ministerio de Ciencia e Innovación/ ; },
abstract = {BACKGROUND: The global burden of antimicrobial resistance demands additional measures to ensure the sustainable and conscious use of antimicrobials. For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. Among them, post-weaning diarrhea causes vast economic losses, as it severely compromises piglets' health and growth performance. In this study, 210 piglets were transferred from a farm with recurrent cases of post-weaning diarrhea to an experimental farm and divided into six different treatment groups to determine the effect of the different treatments on the growth performance and survival, the microbiome, and the resistome in a cross-sectional and longitudinal study. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, and gentamicin, an oral commercial vaccine, a control with water acidification, and an untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. A total of 280 fecal samples from pigs at four different sampling times were selected for metagenomics: before weaning-treatment at the farm of origin, and three days, two weeks, and four weeks post-treatment.

RESULTS: The control group with water acidification showed a reduced death risk in the survival analyses and non-significant differences in average daily weight gain in comparison to the antibiotic-treated groups. However, the growth-promoting effect among antibiotic-treated groups was demonstrated when comparing against the untreated control group at the experimental farm. After four weeks of treatment, diversity indexes revealed significantly decreased diversity for the untreated control and the group that remained at the farm of origin treated with amoxicillin. For this last group, impaired microbial diversity could be related to the continuous amoxicillin treatment carried out at the farm. Analysis of the resistome showed that both gentamicin and amoxicillin treatments significantly contributed to the emergence of resistance, while trimethoprim/sulphonamide and colistin did not, suggesting that different treatments contribute differently to the emergence of resistance.

CONCLUSIONS: Overall, this shotgun longitudinal metagenomics analysis demonstrates that non-antibiotic alternatives, such as water acidification, can contribute to reducing the emergence of antimicrobial resistance without compromising pig growth performance and gut microbiome.},
}

@article {pmid38702505,
year = {2024},
author = {Macdonald, JFH and Pérez-García, P and Schneider, YK and Blümke, P and Indenbirken, D and Andersen, JH and Krohn, I and Streit, WR},
title = {Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10237},
pmid = {38702505},
issn = {2045-2322},
support = {AquaHealth FKZ 031B0945C//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; PlastiSea FKZ 031B0867F//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Cell Wall/metabolism ; *Fucus/metabolism/genetics/microbiology ; *Metagenomics/methods ; Bacteroidetes/genetics/enzymology ; Metagenome ; Microbiota ; Phylogeny ; },
abstract = {Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.},
}

*Cell Wall/metabolism
*Fucus/metabolism/genetics/microbiology
*Metagenomics/methods
Bacteroidetes/genetics/enzymology
Metagenome
Microbiota
Phylogeny

@article {pmid38702151,
year = {2024},
author = {Chen, W and Zhou, H},
title = {Etiological Diagnosis and Treatment Value of mNGS in Alveolar Lavage Fluid of Children with Severe Pneumonia.},
journal = {Alternative therapies in health and medicine},
volume = {},
number = {},
pages = {},
pmid = {38702151},
issn = {1078-6791},
abstract = {OBJECTIVE: Metagenomic sequencing (mNGS) is a promising technique for pathogen detection. However, the use of mNGS in pediatric lung infections is still rarely reported.

METHODS: A total of 59 cases were included between January 2019 and December 2021. To compare the performance of mNGS and routine detection in diagnosing pulmonary infection and identifying pathogenic bacteria.

RESULTS: 59 children (33.90%) were infected with Mycoplasma pneumoniae, 15 were infected with adenovirus type 7 (25.42%), 11 were infected with Streptococcus pneumoniae (18.64%), 6 were infected with Staphylococcus aureus (10.17%), 5 were infected with Klebsiella pneumoniae, Acinetobacter baumannii, pertussis, and oral streptococcus (8.47%), 3 were infected with Haemophilus influenzae (5.08%), and 3 were infected with Pseudomonas aeruginosa (5.08%). Among 59 patients, 41 were co-infected with multiple pathogens and 18 were infected with independent pathogens. Mycoplasma pneumoniae infection was most common in 6 out of 18 independent pathogen patients (33%). Among them were 3 cases of type 7 adenovirus, 53 cases of human herpesvirus (16.7%), and 2 cases of pertussis bacillus (11.1%). One case (5.6%) was infected with Streptococcus pneumoniae, Proteus albicans, Mycobacterium tuberculosis, Staphylococcus aureus, and Klebsiella pneumoniae. In cases where routine testing results are negative, mNGS improves the diagnostic efficiency of mixed pulmonary infections. 17 cases (17/59=28.81%) were diagnosed as single infection through routine testing, and the mNGS results of 4 cases were consistent with routine testing, all of which were Mycoplasma pneumoniae infections. Three cases were tested for partial mNGS matching, of which one case tested positive for Mycoplasma pneumoniae antibody and tested positive for Mycoplasma pneumoniae infection and human infection γ Herpes virus type 4, one case tested positive for antibodies and tested for infection with Mycoplasma pneumoniae and Streptococcus pneumoniae. The routine examination results of the remaining 11 patients were inconsistent with the mNGS examination results. Two patients tested positive for Mycoplasma antibodies. Patient 17 presented with mNGS infection of Haemophilus, Neisseria, and adenovirus type 7, while another patient 18 presented with herpes virus type 5 infection.

CONCLUSION: mNGS is a promising technique for detecting co-pathogens in mixed pediatric lung infections, with potential benefits in terms of speed and sensitivity.},
}

@article {pmid38701980,
year = {2024},
author = {Liu, Z and Cao, S and He, X and Liu, G and Yao, H and Ding, S and Fang, J},
title = {Effects of crayfish shell powder and bamboo-derived biochar on nitrogen conversion, bacterial community and nitrogen functional genes during pig manure composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130783},
doi = {10.1016/j.biortech.2024.130783},
pmid = {38701980},
issn = {1873-2976},
abstract = {This study investigated the effects of crayfish shell powder (CSP) and bamboo-derived biochar (BDB) on nitrogen metabolism, bacterial community and nitrogen functional genes during pig manure composting. Four treatments were established: CP (with no additives), TP1 (5 % BDB), TP2 (5 % CSP) and TP3 (2.5 % BDB + 2.5 % CSP). Compared to CP, the germination index (GI) of TP reached > 85 % 10 days earlier. Meanwhile, TP3 reduced NH3 and N2O emissions by 42.90 % and 65.9 %, respectively, while increased TN (total nitrogen) concentration by 5.43 g/kg. Furthermore, additives changed the bacterial structure and formed a beneficial symbiotic relationship with essential N-preserving bacteria, thereby enhancing nitrogen retention throughout the composting process. Metagenomic analysis revealed that additives upregulated nitrification genes and downregulated denitrification and nitrate reduction genes, ultimately improving nitrogen cycling and mitigating NH3 and N2O emissions. In conclusion, the results confirmed that TP3 was the most effective treatment in reducing nitrogen loss.},
}

@article {pmid38701923,
year = {2024},
author = {Han, Y and Bi, R and Wang, Y and Sun, L and Liu, X and Shi, S and Chang, N and Zhao, L and Bao, J and Xu, Y and Liu, W and Zhang, J and Jiang, N and Zhang, Y and Xu, X and Sun, Y},
title = {Insight into N2O emission and denitrifier communities under different aeration intensities in composting of cattle manure from perspective of multi-factor interaction analysis.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172936},
doi = {10.1016/j.scitotenv.2024.172936},
pmid = {38701923},
issn = {1879-1026},
abstract = {Nitrous oxide (N2O) emission from composting is a significant contributor to greenhouse effect and ozone depletion, which poses a threat to environment. To address the challenge of mitigating N2O emission during composting, this study investigated the response of N2O emission and denitrifier communities (detected by metagenome sequencing) to aeration intensities of 6 L/min (C6), 12 L/min (C12), and 18 L/min (C18) in cattle manure composting using multi-factor interaction analysis. Results showed that N2O emission occurred mainly at mesophilic phase. Cumulative N2O emission (QN2O, 9.79 mg·kg[-1] DW) and total nitrogen loss (TN loss, 16.40 %) in C12 composting treatment were significantly lower than those in the other two treatments. The lower activity of denitrifying enzymes and the more complex and balanced network of denitrifiers and environmental factors might be responsible for the lower N2O emission. Denitrification was confirmed to be the major pathway for N2O production. Moisture content (MC) and Luteimonas were the key factors affecting N2O emission, and nosZ-carrying denitrifier played a significant role in reducing N2O emission. Although relative abundance of nirS was lower than that of nirK significantly (P < 0.05), nirS was the key gene influencing N2O emission. Community composition of denitrifier varied significantly with different aeration treatments (R[2] = 0.931, P = 0.001), and Achromobacter was unique to C12 at mesophilic phase. Physicochemical factors had higher effect on QN2O, whereas denitrifying genes, enzymes and NOX[-] had lower effect on QN2O in C12. The complex relationship between N2O emission and the related factors could be explained by multi-factor interaction analysis more comprehensively. This study provided a novel understanding of mechanism of N2O emission regulated by aeration intensity in composting.},
}

@article {pmid38701655,
year = {2024},
author = {Zhang, Q and Jiang, C and Jiang, L and Qiu, R and Wei, Z and Wu, Q},
title = {Cadmium phytoremediation potential of Houttuynia cordata: Insights from growth, uptake, and rhizosphere mechanisms.},
journal = {Ecotoxicology and environmental safety},
volume = {278},
number = {},
pages = {116417},
doi = {10.1016/j.ecoenv.2024.116417},
pmid = {38701655},
issn = {1090-2414},
abstract = {Cadmium (Cd) pollutes 7.0 % of China's land area. This study examined the potential of Houttuynia cordata for Cd phytoremediation because of its ability to accumulate Cd in its growth matrix. H. cordata were planted in plastic pots filled with paddy field soils having low (LCd), medium (MCd), and high (HCd) Cd levels of 0.19, 0.69, and 2.91 mg/kg, respectively. After six months of growth, harvested plant parts were evaluated for Cd uptake and tolerance mechanisms. Metabolomics and metagenomics approaches were employed to investigate the soil rhizosphere mechanism. Results showed that the average plant biomass increased as soil Cd increased. The biomass Cd contents surpassed the allowable Cd limits for food (≤ 0.2 mg/kg) and medicinal uses (≤ 0.3 mg/kg). Cd contents were higher in H. cordata roots (30.59-86.27 mg/kg) than in other plant parts (0.63-2.90 mg/kg), with significantly increasing values as Cd soil level increased. Phenolic acids, lipids, amino acids and derivatives, organic acids, and alkaloids comprised the majority (69 in MCd vs HCd and 73 % in LCd vs HCd) of the shared upregulated metabolites. In addition, 13 metabolites specific to H. cordata root exudates were significantly increased. The top two principal metabolic pathways were arginine and proline metabolism, and beta-alanine metabolism. H. cordata increased the abundance of Firmicutes and Glomeromycota across all three Cd levels, and also stimulated the growth of Patescibacteria, Rozellomycota, and Claroideoglomus in HCd. Accordingly, H. cordata demonstrated potential for remediation of Cd-contaminated soils, and safety measures for its production and food use must be highly considered.},
}

@article {pmid38701628,
year = {2024},
author = {Marková, K and Kreisinger, J and Vinkler, M},
title = {Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?.},
journal = {Poultry science},
volume = {103},
number = {6},
pages = {103752},
doi = {10.1016/j.psj.2024.103752},
pmid = {38701628},
issn = {1525-3171},
abstract = {Microbiome of the gastrointestinal tract (GIT) has been identified as one of the crucial factors influencing the health and condition of domestic animals. The global poultry industry faces the challenge of understanding the complex relationship between gut microbiota composition and performance-related traits in birds. Considerable variation exists in the results of correlational studies using either 16S rRNA profiling or metagenomics to identify bacterial taxa associated with performance, productivity, or condition in poultry (e.g., body weight, growth rate, feeding efficiency, or egg yield). In this review, we survey the existing reports, discuss variation in research approaches, and identify bacterial taxa consistently linked to improved or deteriorated performance across individual poultry-focused studies. Our survey revealed high methodological heterogeneity, which was in contrast with vastly uniform focus of the research mainly on the domestic chicken (Gallus gallus) as a model. We also show that the bacterial taxa most frequently used in manipulative experiments and commercial probiotics intended for use in poultry (e.g., species of Lactobacillus, Bacillus, Enterococcus, or Bifidobacterium) do not overlap with the bacteria consistently correlated with their improved performance (Candidatus Arthromitus, Methanobrevibacter). Our conclusions urge for increased methodological standardization of the veterinary research in this field. We highlight the need to bridge the gap between correlational results and experimental applications in animal science. To better understand causality in the observed relationships, future research should involve a broader range of host species that includes both agricultural and wild models, as well as a broader range of age groups.},
}

@article {pmid38700829,
year = {2024},
author = {Jang, CS and Kim, H and Kim, D and Han, B},
title = {MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {38700829},
issn = {2092-9293},
abstract = {BACKGROUND: The importance of the human microbiome in the analysis of various diseases is emerging. The two main methods used to profile the human microbiome are 16S rRNA gene sequencing (16S sequencing) and whole-genome shotgun sequencing (WGS). Owing to the full coverage of the genome in sequencing, WGS has multiple advantages over 16S sequencing, including higher taxonomic profiling resolution at the species-level and functional profiling analysis. However, 16S sequencing remains widely used because of its relatively low cost. Although WGS is the standard method for obtaining accurate species-level data, we found that 16S sequencing data contained rich information to predict high-resolution species-level abundances with reasonable accuracy.

OBJECTIVE: In this study, we proposed MicroPredict, a method for accurately predicting WGS-comparable species-level abundance data using 16S taxonomic profile data.

METHODS: We employed a mixed model using two key strategies: (1) modeling both sample- and species-specific information for predicting WGS abundances, and (2) accounting for the possible correlations among different species.

RESULTS: We found that MicroPredict outperformed the other machine learning methods.

CONCLUSION: We expect that our approach will help researchers accurately approximate the species-level abundances of microbiome profiles in datasets for which only cost-effective 16S sequencing has been applied.},
}

@article {pmid38700364,
year = {2024},
author = {Padalko, A and Nair, G and Sousa, FL},
title = {Fusion/fission protein family identification in Archaea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0094823},
doi = {10.1128/msystems.00948-23},
pmid = {38700364},
issn = {2379-5077},
abstract = {The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.},
}

@article {pmid38699479,
year = {2024},
author = {Ma, X and Li, Z and Cai, L and Xiao, M and He, F and Liu, Z and Chen, D and Wang, Y and Shen, L and Gu, Y},
title = {Analysis of fungal diversity in the gut feces of wild takin (Budorcas taxicolor).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1364486},
doi = {10.3389/fmicb.2024.1364486},
pmid = {38699479},
issn = {1664-302X},
abstract = {INTRODUCTION: The composition of the intestinal microbiome correlates significantly with an animal's health status. Hence, this indicator is highly important and sensitive for protecting endangered animals. However, data regarding the fungal diversity of the wild Budorcas taxicolor (takin) gut remain scarce. Therefore, this study analyzes the fungal diversity, community structure, and pathogen composition in the feces of wild B. taxicolor.

METHODS: To ensure comprehensive data analyses, we collected 82 fecal samples from five geographical sites. Amplicon sequencing of the internal transcribed spacer (ITS) rRNA was used to assess fecal core microbiota and potential pathogens to determine whether the microflora composition is related to geographical location or diet. We further validated the ITS rRNA sequencing results via amplicon metagenomic sequencing and culturing of fecal fungi.

RESULTS AND DISCUSSION: The fungal diversity in the feces of wild Budorcas taxicolor primarily comprised three phyla (99.69%): Ascomycota (82.19%), Fungi_unclassified (10.37%), and Basidiomycota (7.13%). At the genus level, the predominant fungi included Thelebolus (30.93%), Functional_unclassified (15.35%), and Ascomycota_unclassified (10.37%). Within these genera, certain strains exhibit pathogenic properties, such as Thelebolus, Cryptococcus, Trichosporon, Candida, Zopfiella, and Podospora. Collectively, this study offers valuable information for evaluating the health status of B. taxicolor and formulating protective strategies.},
}

@article {pmid38699359,
year = {2024},
author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES},
title = {Longitudinal dynamics of the nasopharyngal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their infants.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4257641/v1},
pmid = {38699359},
abstract = {The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest and of clinical relevance. The impact of SARS-CoV-2, the etiological agent of the Coronavirus Disease 2019 (COVID-19) pandemic, on the nasopharyngeal microbiome, particularly among individuals living with HIV, is not fully characterized. Here we describe the nasopharyngeal microbiome before, during and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their infants (18 HIV-exposed, uninfected and 18 HIV-unexposed, uninfected), followed between September 2021 through March 2022. We show using genomic epidemiology that mother and infant dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. Additionally, we used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and infants infected with SARS-CoV-2, 6 infants negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint matched SARS-CoV-2 negative mothers and infants. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- and long-term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and infants had significantly different microbiome composition and bacterial load (p-values <.0001). However, in both mothers and infants, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV-exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.},
}

@article {pmid38699325,
year = {2024},
author = {Witonsky, JI and Elhawary, JR and Eng, C and Oh, SS and Salazar, S and Contreras, MG and Medina, V and Secor, EA and Zhang, P and Everman, JL and Fairbanks-Mahnke, A and Pruesse, E and Sajuthi, SP and Chang, CH and Guerrero, TR and Fuentes, KC and Lopez, N and Montanez-Lopez, CA and Otero, RA and Rivera, RC and Rodriguez, L and Vazquez, G and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Morin, A and Nieves, NA and Rios, C and Serrano, G and Williams, BJM and Ziv, E and Moore, CM and Sheppard, D and Burchard, EG and Seibold, MA and Rodriguez Santana, JR},
title = {The Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes (PRIMERO): Design and Baseline Characteristics for a Birth Cohort Study of Early-life Viral Respiratory Illnesses and Airway Dysfunction in Puerto Rican Children.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.15.24305359},
pmid = {38699325},
abstract = {Epidemiologic studies demonstrate an association between early-life respiratory illnesses (RIs) and the development of childhood asthma. However, it remains uncertain whether these children are predisposed to both conditions or if early-life RIs induce alterations in airway function, immune responses, or other human biology that contribute to the development of asthma. Puerto Rican children experience a disproportionate burden of early-life RIs and asthma, making them an important population for investigating this complex interplay. PRIMERO, the Puerto Rican Infant Metagenomics and Epidemiologic Study of Respiratory Outcomes , recruited pregnant women and their newborns to investigate how the airways develop in early life among infants exposed to different viral RIs, and will thus provide a critical understanding of childhood asthma development. As the first asthma birth cohort in Puerto Rico, PRIMERO will prospectively follow 2,100 term healthy infants. Collected samples include post-term maternal peripheral blood, infant cord blood, the child's peripheral blood at the year two visit, and the child's nasal airway epithelium, collected using minimally invasive nasal swabs, at birth, during RIs over the first two years of life, and at annual healthy visits until age five. Herein, we describe the study's design, population, recruitment strategy, study visits and procedures, and primary outcomes.},
}

@article {pmid38699315,
year = {2024},
author = {Langelier, C and Chu, V and Glascock, A and Donnell, D and Grabow, C and Brown, C and Ward, R and Love, C and Kalantar, K and Cohen, S and Cannon, C and Woodworth, M and Kelley, C and Celum, C and Luetkemeyer, A},
title = {Doxycycline post-exposure prophylaxis for sexually transmitted infections impacts the gut antimicrobial resistome.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4243341/v1},
pmid = {38699315},
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections (STIs) among men who have sex with men and transgender women. While poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from a randomized clinical trial who either received doxy-PEP as a one-time doxycycline 200 mg taken after condomless sex (DP arm, n = 100) or standard of care treatment (SOC arm, n = 50). From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data was analyzable from 127 samples derived from 89 participants, and RNA-seq data from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. Tetracycline ARGs were detected in all day-0 DNA-seq samples and 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46-51% in the metagenome (p = 0.02) and 4-15% in the metatranscriptome (p < 0.01), but no changes in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, p < 0.01) and metatranscriptome (Spearman's ρ = 0.55, p < 0.01). Bacterial microbiome alpha diversity, beta diversity, and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome, and an increase in the expression of tetracycline ARGs. Notably, doxy-PEP did not significantly alter alpha diversity or taxonomic composition of the gut microbiome, and did not demonstrate significant increases in non-tetracycline ARG classes. Further studies and population level surveillance are needed to understand the implications of these findings as doxy-PEP is implemented as a public health strategy.},
}

@article {pmid38699305,
year = {2024},
author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES},
title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4257515/v1},
pmid = {38699305},
abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that while the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). However, gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.},
}

@article {pmid38699231,
year = {2024},
author = {de Oliveira, AR and de Toledo Rós, B and Jardim, R and Kotowski, N and de Barros, A and Pereira, RHG and Almeida, NF and Dávila, AMR},
title = {A comparative genomics study of the microbiome and freshwater resistome in Southern Pantanal.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1352801},
doi = {10.3389/fgene.2024.1352801},
pmid = {38699231},
issn = {1664-8021},
abstract = {This study explores the resistome and bacterial diversity of two small lakes in the Southern Pantanal, one in Aquidauana sub-region, close to a farm, and one in Abobral sub-region, an environmentally preserved area. Shotgun metagenomic sequencing data from water column samples collected near and far from the floating macrophyte Eichhornia crassipes were used. The Abobral small lake exhibited the highest diversity and abundance of antibiotic resistance genes (ARGs), antibiotic resistance classes (ARGCs), phylum, and genus. RPOB2 and its resistance class, multidrug resistance, were the most abundant ARG and ARGC, respectively. Pseudomonadota was the dominant phylum across all sites, and Streptomyces was the most abundant genus considering all sites.},
}

@article {pmid38699181,
year = {2024},
author = {Md Lasim, A and Mohd Ngesom, AM and Nathan, S and Abdul Razak, F and Abdul Halim, M and Mohd-Saleh, W and Zainul Abidin, K and Mohd-Taib, FS},
title = {Bacterial community profiles within the water samples of leptospirosis outbreak areas.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17096},
doi = {10.7717/peerj.17096},
pmid = {38699181},
issn = {2167-8359},
mesh = {*Leptospirosis/epidemiology/microbiology/transmission ; Humans ; *Water Microbiology ; *Disease Outbreaks ; *RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Leptospira/genetics/isolation & purification ; Bacteria/isolation & purification/genetics/classification ; High-Throughput Nucleotide Sequencing ; Animals ; },
abstract = {BACKGROUND: Leptospirosis is a water-related zoonotic disease. The disease is primarily transmitted from animals to humans through pathogenic Leptospira bacteria in contaminated water and soil. Rivers have a critical role in Leptospira transmissions, while co-infection potentials with other waterborne bacteria might increase the severity and death risk of the disease.

METHODS: The water samples evaluated in this study were collected from four recreational forest rivers, Sungai Congkak, Sungai Lopo, Hulu Perdik, and Gunung Nuang. The samples were subjected to next-generation sequencing (NGS) for the 16S rRNA and in-depth metagenomic analysis of the bacterial communities.

RESULTS: The water samples recorded various bacterial diversity. The samples from the Hulu Perdik and Sungai Lopo downstream sampling sites had a more significant diversity, followed by Sungai Congkak. Conversely, the upstream samples from Gunung Nuang exhibited the lowest bacterial diversity. Proteobacteria, Firmicutes, and Acidobacteria were the dominant phyla detected in downstream areas. Potential pathogenic bacteria belonging to the genera Burkholderiales and Serratia were also identified, raising concerns about co-infection possibilities. Nevertheless, Leptospira pathogenic bacteria were absent from all sites, which is attributable to its limited persistence. The bacteria might also be washed to other locations, contributing to the reduced environmental bacterial load.

CONCLUSION: The present study established the presence of pathogenic bacteria in the river ecosystems assessed. The findings offer valuable insights for designing strategies for preventing pathogenic bacteria environmental contamination and managing leptospirosis co-infections with other human diseases. Furthermore, closely monitoring water sample compositions with diverse approaches, including sentinel programs, wastewater-based epidemiology, and clinical surveillance, enables disease transmission and outbreak early detections. The data also provides valuable information for suitable treatments and long-term strategies for combating infectious diseases.},
}

*Leptospirosis/epidemiology/microbiology/transmission
Humans
*Water Microbiology
*Disease Outbreaks
*RNA, Ribosomal, 16S/genetics
*Rivers/microbiology
Leptospira/genetics/isolation & purification
Bacteria/isolation & purification/genetics/classification
High-Throughput Nucleotide Sequencing
Animals

@article {pmid38699060,
year = {2024},
author = {Liu, XJA and Han, S and Frey, SD and Melillo, JM and Zhou, J and DeAngelis, KM},
title = {Microbial responses to long-term warming differ across soil microenvironments.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae051},
doi = {10.1093/ismeco/ycae051},
pmid = {38699060},
issn = {2730-6151},
abstract = {Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.},
}

@article {pmid38698785,
year = {2024},
author = {Wang, C and Wei, N and Zhang, M and Zhang, X},
title = {Pulmonary infection with Aeromonas dhakensis in a patient with acute T lymphoblastic leukemia: a case report and review of the literature.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1357714},
doi = {10.3389/fmed.2024.1357714},
pmid = {38698785},
issn = {2296-858X},
abstract = {BACKGROUND: Aeromonas dhakensis is a gram-negative bacterium. In recent years, Aeromonas dhakensis has gradually attracted increasing attention due to its strong virulence and poor prognosis. Clinical reports of pulmonary infection caused by Aeromonas dhakensis are rare.

CASE PRESENTATION: A patient with acute T lymphoblastic leukemia experienced myelosuppression after chemotherapy, developed a secondary pulmonary infection with Aeromonas dhakensis and was hospitalized due to fever. The patient underwent testing for inflammatory markers, chest imaging, blood culture, bronchoalveolar lavage, pleural drainage, and metagenomic next-generation sequencing of alveolar lavage fluid and pleural fluid to obtain evidence of Aeromonas dhakensis infection, and was treated with four generations of cephalosporin combined with fluoroquinolone antibiotics. The patient's condition significantly improved.

DISCUSSION: Among pulmonary infectious pathogens, Aeromonas dhakensis is relatively rare. Once an Aeromonas strain is cultured in the clinical work, pathogenic sequencing should be performed on the detected samples for early accurate diagnosis and effective anti-infection treatment.},
}

@article {pmid38698421,
year = {2024},
author = {Alshammari, A and Alotaibi, J and Almaghrabi, R and Bawazeer, R and Althawadi, S and Tayeb, H},
title = {First parechovirus reported case in Saudi Arabia in hospitalized immunocompromised adult patient.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {102},
pmid = {38698421},
issn = {1743-422X},
mesh = {Humans ; Female ; Middle Aged ; *Immunocompromised Host ; *Picornaviridae Infections/virology/diagnosis ; *Parechovirus/genetics/isolation & purification/classification ; Saudi Arabia ; High-Throughput Nucleotide Sequencing ; Glioblastoma/virology ; Metagenomics ; Encephalitis, Viral/virology/diagnosis ; Herpesvirus 1, Human/genetics/isolation & purification ; Hospitalization ; },
abstract = {Human parechovirus, a member of the Picornaviridae family (PeVs), can lead to severe infections, including severe meningitis, meningoencephalitis, and sepsis-like syndrome. We report a case of human parechovirus-related encephalitis in a 52-year-old woman diagnosed with glioblastoma multiforme. She underwent surgical resection in June 2022. Unfortunately, her disease recurred, and she underwent a second resection in August 2022, followed by radiation therapy and Temozolomide therapy. She presented to the hospital with acute confusion followed by seizures, necessitating intubation for airway support. A cerebrospinal fluid (CSF) sample was obtained and processed using the Biofire FilmArray, which reported the detection of HSV-1. Despite being on Acyclovir, the patient did not show signs of improvement. Consequently, a second CSF sample was obtained and sent for next-generation sequencing (NGS), which returned a positive result for Parechovirus. In this presented case, the patient exhibited symptoms of an unknown infectious cause. The utilization of NGS and metagenomic analysis helped identify Parechovirus as the primary pathogen present, in addition to previously identified HSV. This comprehensive approach facilitated a thorough assessment of the underlying infection and guided targeted treatment. In conclusion, the application of NGS techniques and metagenomic analysis proved instrumental in identifying the root cause of the infection.},
}

Humans
Female
Middle Aged
*Immunocompromised Host
*Picornaviridae Infections/virology/diagnosis
*Parechovirus/genetics/isolation & purification/classification
Saudi Arabia
High-Throughput Nucleotide Sequencing
Glioblastoma/virology
Metagenomics
Encephalitis, Viral/virology/diagnosis
Herpesvirus 1, Human/genetics/isolation & purification
Hospitalization

@article {pmid38698035,
year = {2024},
author = {Bhoobalan-Chitty, Y and Xu, S and Martinez-Alvarez, L and Karamycheva, S and Makarova, KS and Koonin, EV and Peng, X},
title = {Regulatory sequence-based discovery of anti-defense genes in archaeal viruses.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3699},
pmid = {38698035},
issn = {2041-1723},
support = {NNF21OC0067491//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17OC0031154//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; DFF-0135-00402//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; },
mesh = {*Archaeal Viruses/genetics ; *Archaea/genetics/virology/immunology ; Promoter Regions, Genetic/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Viral Proteins/genetics ; Archaeal Proteins/genetics/metabolism ; Metagenome/genetics ; CRISPR-Associated Proteins/genetics/metabolism ; CRISPR-Cas Systems/genetics ; },
abstract = {In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.},
}

*Archaeal Viruses/genetics
*Archaea/genetics/virology/immunology
Promoter Regions, Genetic/genetics
Clustered Regularly Interspaced Short Palindromic Repeats/genetics
Regulatory Sequences, Nucleic Acid/genetics
Viral Proteins/genetics
Archaeal Proteins/genetics/metabolism
Metagenome/genetics
CRISPR-Associated Proteins/genetics/metabolism
CRISPR-Cas Systems/genetics

@article {pmid38697552,
year = {2024},
author = {Song, K and Wang, S and Xu, X and Ma, J and Yang, Y and Zeng, Y and Li, J and Zhou, X and Zhou, Y},
title = {Benthic clade II-type nitrous oxide reducers suppress nitrous oxide emissions in shallow lakes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172908},
doi = {10.1016/j.scitotenv.2024.172908},
pmid = {38697552},
issn = {1879-1026},
abstract = {Shallow lakes, recognized as hotspots for nitrogen cycling, contribute to the emission of the potent greenhouse gas nitrous oxide (N2O), but the current emission estimates for this gas have a high degree of uncertainty. However, the role of N2O-reducing bacteria (N2ORB) as N2O sinks and their contribution to N2O reduction in aquatic ecosystems in response to N2O dynamics have not been determined. Here, we investigated the N2O dynamics and microbial processes in the nitrogen cycle, which included both N2O production and consumption, in five shallow lakes spanning approximately 500 km. The investigated sites exhibited N2O oversaturation, with excess dissolved N2O concentrations (ΔN2O) ranging from 0.55 ± 0.61 to 53.17 ± 15.75 nM. Sediment-bound N2O (sN2O) was significantly positively correlated with the nitrate concentration in the overlying water (p < 0.05), suggesting that nitrate accumulation contributes to benthic N2O generation. High N2O consumption activity (RN2O) corresponded to low ΔN2O. In addition, a significant negative correlation was found between RN2O and nir/nosZ, showing that bacteria encoding nosZ contributed to N2O consumption in the benthic sediments. Redundancy analysis indicated that benthic functional genes effectively reflected the variations in RN2O and ∆N2O. qPCR analysis revealed that the clade II nosZ gene was more sensitive to ΔN2O than the clade I nosZ gene. Furthermore, four novel genera of potential nondenitrifying N2ORB were identified based on metagenome-assembled genome analysis. These genera, which are affiliated with clade II, lack genes responsible for N2O production. Collectively, benthic N2ORB, especially for clade II-type N2ORB, harnesses N2O consumption activity leading to low N2O emissions from shallow lakes. This study advances our knowledge of the role of benthic clade II-type N2ORB in regulating N2O emissions in shallow lakes.},
}

@article {pmid38697527,
year = {2024},
author = {Zhu, W and Zhao, H and Ke, J and Zhang, J and Liu, X and Zhou, Y and Chen, R and Wang, A and Li, X},
title = {Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172897},
doi = {10.1016/j.scitotenv.2024.172897},
pmid = {38697527},
issn = {1879-1026},
abstract = {Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signals and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.},
}

@article {pmid38697408,
year = {2024},
author = {Dong, B and Peng, Y and Wang, M and Peng, C and Li, X},
title = {Multi-omics integrated analysis indicated that non-polysaccharides of Sijunzi decoction ameliorated spleen deficiency syndrome via regulating microbiota-gut-metabolites axis and exerted synergistic compatibility.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118276},
doi = {10.1016/j.jep.2024.118276},
pmid = {38697408},
issn = {1872-7573},
abstract = {As a classical traditional Chinese medicine formula to invigorating spleen and replenishing qi, Sijunzi decoction (SJZD) is composed of four herbs, which is applied to cure spleen deficiency syndrome (SDS) clinically. The non-polysaccharides (NPSs) of SJZD (SJZD_NPS) are important pharmacodynamic material basis. However, the amelioration mechanism of SJZD_NPS on SDS has not been fully elaborated. Additionally, the contribution of herbs compatibility to efficacy of this formula remains unclear.

AIM OF THE STUDY: The aim was to explore the underlying mechanisms of SJZD_NPS on improving SDS, and uncover the scientific connotation in SJZD compatibility.

MATERIALS AND METHODS: A strategy integrating incomplete formulae (called "Chai-fang" in Chinese) comparison, pharmacodynamics, gut microbiome, and metabolome was employed to reveal the role of each herb to SJZD compatibility against SDS. Additionally, the underlying mechanism harbored by SJZD_NPS was further explored through targeted metabolomics, network pharmacology, molecular docking, pseudo-sterile model, and metagenomics.

RESULTS: SJZD_NPS significantly alleviated diarrhea, disordered secretion of gastrointestinal hormones and neurotransmitters, damage of ileal morphology and intestinal barrier in SDS rats, which was superior to the NPSs of Chai-fang. 16S rRNA gene sequencing and metabolomics analysis revealed that SJZD_NPS effectively restored the disturbed gut microbiota community and abnormal metabolism caused by SDS, showing the most evident recovery. Moreover, SJZD_NPS recalled the levels of partial amino acids, short chain fatty acids and bile acids, which possessed strong binding affinity towards potential targets. The depletion of gut microbiota confirmed that the SDS-amelioration efficacy of SJZD_NPS is dependent on the intact gut microbiome, with the relative abundance of potential probiotics such as Lactobacillus_johnsonii and Lactobacillus_taiwanensis been enriched.

CONCLUSION: NPSs in SJZD can improve SDS-induced gastrointestinal-nervous system dysfunction through regulating microbiota-gut-metabolites axis, with four herbs exerting synergistic effects, which indicated the compatibility rationality of SJZD.},
}

@article {pmid38696985,
year = {2024},
author = {da Silva Duarte, V and de Paula Dias Moreira, L and Skeie, SB and Svalestad, F and Øyaas, J and Porcellato, D},
title = {Database selection for shotgun metaproteomic of low-diversity dairy microbiomes.},
journal = {International journal of food microbiology},
volume = {418},
number = {},
pages = {110706},
doi = {10.1016/j.ijfoodmicro.2024.110706},
pmid = {38696985},
issn = {1879-3460},
abstract = {The metaproteomics field has recently gained more and more interest as a valuable tool for studying both the taxonomy and function of microbiomes, including those used in food fermentations. One crucial step in the metaproteomics pipeline is selecting a database to obtain high-quality taxonomical and functional information from microbial communities. One of the best strategies described for building protein databases is using sample-specific or study-specific protein databases obtained from metagenomic sequencing. While this is true for high-diversity microbiomes (such as gut and soil), there is still a lack of validation for different database construction strategies in low-diversity microbiomes, such as those found in fermented dairy products where starter cultures containing few species are used. In this study, we assessed the performance of various database construction strategies applied to metaproteomics on two low-diversity microbiomes obtained from cheese production using commercial starter cultures and analyzed by LC-MS/MS. Substantial differences were detected between the strategies, and the best performance in terms of the number of peptides and proteins identified from the spectra was achieved by metagenomic-derived databases. However, extensive databases constructed from a high number of available online genomes obtained a similar taxonomical and functional annotation of the metaproteome compared to the metagenomic-derived databases. Our results indicate that, in the case of low-diversity dairy microbiomes, the use of publically available genomes to construct protein databases can be considered as an alternative to metagenome-derived databases.},
}

@article {pmid38696336,
year = {2024},
author = {Gauthier, NPG and Chan, W and Locher, K and Smailus, D and Coope, R and Charles, M and Jassem, A and Kopetzky, J and Chorlton, SD and Manges, AR},
title = {Validation of an automated, end-to-end metagenomic sequencing assay for agnostic detection of respiratory viruses.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae226},
pmid = {38696336},
issn = {1537-6613},
abstract = {BACKGROUND: Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translational barriers prohibit the widespread adoption of this technology in clinical laboratories. We validate an end-to-end mNGS assay for detection of respiratory viruses. Our assay is optimized to reduce turnaround time, lower cost-per-sample, increase throughput, and deploy secure and actionable bioinformatic results.

METHODS: We validated our assay using residual nasopharyngeal swab specimens from Vancouver General Hospital (n = 359), RT-PCR-positive, or negative for Influenza, SARS-CoV-2, and RSV. We quantified sample stability, assay precision, the effect of background nucleic acid levels, and analytical limits of detection. Diagnostic performance metrics were estimated.

RESULTS: We report that our mNGS assay is highly precise, semi-quantitative, with analytical limits of detection ranging from 103-104 copies/mL. Our assay is highly specific (100%) and sensitive (61.9% Overall: 86.8%; RT-PCR Ct < 30). Multiplexing capabilities enable processing of up to 55-specimens simultaneously on an Oxford Nanopore GridION device, with results reported within 12-hours.

CONCLUSIONS: This study outlines the diagnostic performance and feasibility of mNGS for respiratory viral diagnostics, infection control, and public health surveillance. We addressed translational barriers to widespread mNGS adoption.},
}

@article {pmid38695096,
year = {2024},
author = {Liu, H and Zhao, X and Xu, S and Zhao, L and Han, X and Xu, X and Zhao, N and Hu, L and Luo, C and Wang, X and Zhang, Q and Guo, T},
title = {Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12830},
pmid = {38695096},
issn = {1749-4877},
support = {32100100//Youth Fund Project of National Natural Science Foundation of China/ ; 2022-ZJ-943Q//National Science Foundation of Qinghai Province/ ; LHZX-2022-02//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; },
abstract = {The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.},
}

@article {pmid38695019,
year = {2024},
author = {Luo, D and Dai, L},
title = {A 26-year-old man with multiple organ failure caused by Aeromonas dhakensis infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1289338},
doi = {10.3389/fmed.2024.1289338},
pmid = {38695019},
issn = {2296-858X},
abstract = {BACKGROUND: Infections in humans are mainly caused by Aeromonas hydrophila, Aeromonas caviae, and Aeromonas veronii. In recent years, Aeromonas dhakensis has been recognized as widely distributed in the environment, with strong virulence. However, this bacterial infection usually does not appear in patients with pneumonia as the first symptom.

CASE REPORT: We report a 26-year-old man who was admitted to the hospital with community-acquired pneumonia as the first symptom and developed serious conditions such as hemolytic uremic syndrome, multiple organ dysfunction, and hemorrhagic shock within a short period. He died after 13 h of admission, and the subsequent metagenomic-next generation sequencing test confirmed the finally identified pathogen of infection as A. dhakensis.

CONCLUSION: Aeromonas is a rare pathogen identified in the diagnosis of community-acquired pneumonia. Hence, doctors need to develop their experience in identifying the difference between infections caused by pathogenic microorganisms. Medical attention is essential during the occurrence of respiratory symptoms that could be controlled by empirical drugs, such as cephalosporins or quinolones. When patients with community-acquired pneumonia present hemoptysis and multiple organ dysfunction in clinical treatment, an unusual pathogen infection should be considered, and the underlying etiology should be clarified at the earliest for timely treatment.},
}

@article {pmid38694799,
year = {2024},
author = {Zhang, Y and Xue, G and Wang, F and Zhang, J and Xu, L and Yu, C},
title = {The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1382332},
doi = {10.3389/fmicb.2024.1382332},
pmid = {38694799},
issn = {1664-302X},
abstract = {BACKGROUND: While antibiotics are commonly used to treat inflammatory bowel disease (IBD), their widespread application can disturb the gut microbiota and foster the emergence and spread of antibiotic resistance. However, the dynamic changes to the human gut microbiota and direction of resistance gene transmission under antibiotic effects have not been clearly elucidated.

METHODS: Based on the Human Microbiome Project, a total of 90 fecal samples were collected from 30 IBD patients before, during and after antibiotic treatment. Through the analysis workflow of metagenomics, we described the dynamic process of changes in bacterial communities and resistance genes pre-treatment, during and post-treatment. We explored potential consistent relationships between gut microbiota and resistance genes, and established gene transmission networks among species before and after antibiotic use.

RESULTS: Exposure to antibiotics can induce alterations in the composition of the gut microbiota in IBD patients, particularly a reduction in probiotics, which gradually recovers to a new steady state after cessation of antibiotics. Network analyses revealed intra-phylum transfers of resistance genes, predominantly between taxonomically close organisms. Specific resistance genes showed increased prevalence and inter-species mobility after antibiotic cessation.

CONCLUSION: This study demonstrates that antibiotics shape the gut resistome through selective enrichment and promotion of horizontal gene transfer. The findings provide insights into ecological processes governing resistance gene dynamics and dissemination upon antibiotic perturbation of the microbiota. Optimizing antibiotic usage may help limit unintended consequences like increased resistance in gut bacteria during IBD management.},
}

@article {pmid38694752,
year = {2024},
author = {Brame, JE and Liddicoat, C and Abbott, CA and Edwards, RA and Robinson, JM and Gauthier, NE and Breed, MF},
title = {The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11239},
doi = {10.1002/ece3.11239},
pmid = {38694752},
issn = {2045-7758},
abstract = {Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.},
}

@article {pmid38694516,
year = {2024},
author = {Sabat, AJ and Durfee, T and Baldwin, S and Akkerboom, V and Voss, A and Friedrich, AW and Bathoorn, E},
title = {The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1368923},
doi = {10.3389/fcimb.2024.1368923},
pmid = {38694516},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *Genome, Bacterial ; *High-Throughput Nucleotide Sequencing ; *Mycoplasma/genetics/isolation & purification/classification ; Mycoplasma Infections/microbiology/diagnosis ; Whole Genome Sequencing/methods ; Lung Transplantation ; Prophages/genetics ; Interspersed Repetitive Sequences/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; },
abstract = {INTRODUCTION: Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.

METHODS: This study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.

RESULTS: Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination.

CONCLUSION: This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.},
}

Humans
*Metagenomics/methods
*Genome, Bacterial
*High-Throughput Nucleotide Sequencing
*Mycoplasma/genetics/isolation & purification/classification
Mycoplasma Infections/microbiology/diagnosis
Whole Genome Sequencing/methods
Lung Transplantation
Prophages/genetics
Interspersed Repetitive Sequences/genetics
Anti-Bacterial Agents/pharmacology/therapeutic use

@article {pmid38693138,
year = {2024},
author = {Jeilu, O and Alexandersson, E and Johansson, E and Simachew, A and Gessesse, A},
title = {A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10012},
pmid = {38693138},
issn = {2045-2322},
mesh = {*beta-Glucosidase/genetics/metabolism/chemistry ; *Lakes/microbiology ; *Biomass ; Metagenomics/methods ; Escherichia coli/genetics/metabolism ; Metagenome ; Cloning, Molecular ; Enzyme Stability ; Hydrolysis ; Hydrogen-Ion Concentration ; Cellulose/metabolism ; Temperature ; Glucose/metabolism ; },
abstract = {Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu[2+] and Mn[2+] ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.},
}

*beta-Glucosidase/genetics/metabolism/chemistry
*Lakes/microbiology
*Biomass
Metagenomics/methods
Escherichia coli/genetics/metabolism
Metagenome
Cloning, Molecular
Enzyme Stability
Hydrolysis
Hydrogen-Ion Concentration
Cellulose/metabolism
Temperature
Glucose/metabolism

@article {pmid38692845,
year = {2024},
author = {Guadalupe, JJ and Pazmiño-Vela, M and Pozo, G and Vernaza, W and Ochoa-Herrera, V and Torres, ML and Torres, AF},
title = {Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13272},
doi = {10.1111/1758-2229.13272},
pmid = {38692845},
issn = {1758-2229},
support = {//Universidad San Francisco de Quito Collaboration Grant/ ; },
mesh = {Ecuador ; *Wastewater/microbiology ; *Microbial Consortia/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microalgae/classification/metabolism ; Water Purification ; Biodegradation, Environmental ; Metagenome ; },
abstract = {Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.},
}

Ecuador
*Wastewater/microbiology
*Microbial Consortia/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Metagenomics
Microalgae/classification/metabolism
Water Purification
Biodegradation, Environmental
Metagenome

@article {pmid38692373,
year = {2024},
author = {Yin, W and Li, Y and Xu, W and Bao, Y and Zhu, J and Su, X and Han, J and Chen, C and Lin, H and Sun, F},
title = {Unveiling long-term combined effect of salinity and Lead(II) on anammox activity and microbial community dynamics in saline wastewater treatment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130767},
doi = {10.1016/j.biortech.2024.130767},
pmid = {38692373},
issn = {1873-2976},
abstract = {The study assessed the effect of salinity and lead (Pb(II)) on the anammox sludge for nitrogen removal from saline wastewater. Results showed decreased nitrogen removal and specific anammox activity (SAA) with elevated salinity and Pb(II). SAA reduced from 541.3 ± 4.3 mg N g[-1] VSS d[-1] at 0.5 mg/L Pb(II) to 436.0 ± 0.2 mg N g[-1] VSS d[-1] at 30 g/L NaCl, further to 303.6 ± 7.1 mg N g[-1] VSS d[-1] under 30 g/L NaCl + 0.5 mg/L Pb(II). Notably, the combined inhibition at salinity (15-20 g/L NaCl) and Pb(II) (0.3-0.4 mg/L) exhibited synergistic effect, while higher salinity and Pb(II) aligned with independent inhibition models. Combined inhibition decreased protein/polysaccharides ratio, indicating more severe negative effect on anammox aggregation capacity. Metagenomics confirmed decreased Candidatus Kuenenia, and enhanced denitrification under elevated salinity and Pb(II) conditions. This study offers insights into anammox operation for treating saline wastewater with heavy metals.},
}

@article {pmid38692260,
year = {2024},
author = {Dai, B and Yang, Y and Wang, Z and Zhou, J and Wang, Z and Zhang, X and Xia, S},
title = {Refractory dissolved organic matters in sludge leachate trigger the combination of anammox and denitratation for advanced nitrogen removal.},
journal = {Water research},
volume = {257},
number = {},
pages = {121678},
doi = {10.1016/j.watres.2024.121678},
pmid = {38692260},
issn = {1879-2448},
abstract = {The cost-effective treatment of sludge leachate (SL) with high nitrogen content and refractory dissolved organic matter (rDOM) has drawn increasing attention. This study employed, for the first time, a rDOM triggered denitratation-anammox continuous-flow process to treat landfill SL. Moreover, the mechanisms of exploiting rDOM from SL as an inner carbon source for denitratation were systematically analyzed. The results demonstrated outstanding nitrogen and rDOM removal performance without any external carbon source supplement. In this study, effluent concentrations of 4.27 ± 0.45 mgTIN/L and 5.58 ± 1.64 mgTN/L were achieved, coupled with an impressive COD removal rate of 65.17 % ± 1.71 %. The abundance of bacteria belonging to the Anaerolineaceae genus, which were identified as rDOM degradation bacteria, increased from 18.23 % to 35.62 %. As a result, various types of rDOM were utilized to different extents, with proteins being the most notable, except for lignins. Metagenomic analysis revealed a preference for directing electrons towards NO3[-]-N reductase rather than NO2[-]-N reductase, indicating the coupling of denitratation bacteria and anammox bacteria (Candidatus Brocadia). Overall, this study introduced a novel synergy platform for advanced nitrogen removal in treating SL using its inner carbon source. This approach is characterized by low energy consumption and operational costs, coupled with commendable efficiency.},
}

@article {pmid38692150,
year = {2024},
author = {Cai, Y and Chen, C and Sun, T and Li, G and Wang, W and Zhao, H and An, T},
title = {Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108704},
doi = {10.1016/j.envint.2024.108704},
pmid = {38692150},
issn = {1873-6750},
abstract = {With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.},
}

@article {pmid38691556,
year = {2024},
author = {Kawser, AQMR and Hoque, MN and Rahman, MS and Sakif, TI and Coffey, TJ and Islam, T},
title = {Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303047},
doi = {10.1371/journal.pone.0303047},
pmid = {38691556},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Gastrointestinal Microbiome/genetics ; *Fishes/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; },
abstract = {The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.},
}

Animals
Bangladesh
*Gastrointestinal Microbiome/genetics
*Fishes/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/isolation & purification
Biodiversity
Phylogeny

@article {pmid38691513,
year = {2024},
author = {Kantor, RS and Jiang, M},
title = {Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02638},
pmid = {38691513},
issn = {1520-5851},
abstract = {Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing for specific pathogens (e.g., SARS-CoV-2). In the past three years, researchers have expanded sequencing to monitor a broad range of pathogens, applying probe capture enrichment to wastewater. The goals of those studies included (1) monitoring and expanding fundamental knowledge of disease dynamics for known pathogens and (2) evaluating the potential for early detection of emerging diseases resulting from zoonotic spillover or novel viral variants. Several studies using off-the-shelf probe panels designed for clinical and environmental surveillance reported that enrichment increased virus relative abundance but did not recover complete genomes for most nonenteric viruses. Based on our experience and recent results reported by others using these panels for wastewater, clinical, and synthetic samples, we discuss challenges and technical factors that affect the rates of false positive and false negative results. We identify trade-offs and opportunities throughout the workflow, including in wastewater sample processing, probe panel design, and bioinformatic analysis. We suggest tailored methods of virus concentration and background removal, carefully designed probe panels, and multithresholded bioinformatics analysis.},
}

@article {pmid38690990,
year = {2024},
author = {Chen, P and Chen, H and Liu, Z and Pan, X and Liu, Q and Yang, X},
title = {Fungal-bacteria interactions provide shelter for bacteria in Caesarean section scar diverticulum.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.90363},
pmid = {38690990},
issn = {2050-084X},
support = {2023A1515012940//Natural Science Foundation of Guangdong Province/ ; 2023A1515110325//Guangdong Basic and Applied Basic Research Foundation/ ; GZC20233216//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Female ; *Cesarean Section/adverse effects ; Humans ; *Diverticulum/microbiology/metabolism ; *Bacteria/metabolism/genetics ; *Cicatrix/microbiology/metabolism ; Dysbiosis/microbiology ; Fungi/metabolism/genetics/physiology ; Microbial Interactions ; Microbiota ; },
abstract = {Caesarean section scar diverticulum (CSD) is a significant cause of infertility among women who have previously had a Caesarean section, primarily due to persistent inflammatory exudation associated with this condition. Even though abnormal bacterial composition is identified as a critical factor leading to this chronic inflammation, clinical data suggest that a long-term cure is often unattainable with antibiotic treatment alone. In our study, we employed metagenomic analysis and mass spectrometry techniques to investigate the fungal composition in CSD and its interaction with bacteria. We discovered that local fungal abnormalities in CSD can disrupt the stability of the bacterial population and the entire microbial community by altering bacterial abundance via specific metabolites. For instance, Lachnellula suecica reduces the abundance of several Lactobacillus spp., such as Lactobacillus jensenii, by diminishing the production of metabolites like Goyaglycoside A and Janthitrem E. Concurrently, Clavispora lusitaniae and Ophiocordyceps australis can synergistically impact the abundance of Lactobacillus spp. by modulating metabolite abundance. Our findings underscore that abnormal fungal composition and activity are key drivers of local bacterial dysbiosis in CSD.},
}

Female
*Cesarean Section/adverse effects
Humans
*Diverticulum/microbiology/metabolism
*Bacteria/metabolism/genetics
*Cicatrix/microbiology/metabolism
Dysbiosis/microbiology
Fungi/metabolism/genetics/physiology
Microbial Interactions
Microbiota

@article {pmid38690913,
year = {2024},
author = {Chen, Y and Dong, X and Sun, Z and Xu, C and Zhang, X and Qin, S and Geng, W and Cao, H and Zhai, B and Li, X and Wu, N},
title = {Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0349023},
doi = {10.1128/spectrum.03490-23},
pmid = {38690913},
issn = {2165-0497},
abstract = {The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.},
}

@article {pmid38690316,
year = {2024},
author = {Rivera-Lopez, EO and Nieves-Morales, R and Melendez-Martinez, G and Paez-Diaz, JA and Rodriguez-Carrio, SM and Rodriguez-Ramos, J and Morales-Valle, L and Rios-Velazquez, C},
title = {Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110421},
doi = {10.1016/j.dib.2024.110421},
pmid = {38690316},
issn = {2352-3409},
abstract = {The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.},
}

@article {pmid38689852,
year = {2024},
author = {Wang, T and Luo, Y and Kong, X and Yu, B and Zheng, P and Huang, Z and Mao, X and Yu, J and Luo, J and Yan, H and He, J},
title = {Genetic- and fiber-diet-mediated changes in virulence factors in pig colon contents and feces and their driving factors.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1351962},
doi = {10.3389/fvets.2024.1351962},
pmid = {38689852},
issn = {2297-1769},
abstract = {Virulence factors (VFs) are key factors for microorganisms to establish defense mechanisms in the host and enhance their pathogenic potential. However, the spectrum of virulence factors in pig colon and feces, as well as the influence of dietary and genetic factors on them, remains unreported. In this study, we firstly revealed the diversity, abundance and distribution characteristics of VFs in the colonic contents of different breeds of pigs (Taoyuan, Xiangcun and Duroc pig) fed with different fiber levels by using a metagenomic analysis. The analysis resulted in the identification of 1,236 virulence factors, which could be grouped into 16 virulence features. Among these, Taoyuan pigs exhibited significantly higher levels of virulence factors compared to Duroc pigs. The high-fiber diet significantly reduced the abundance of certain virulence factor categories, including iron uptake systems (FbpABC, HitABC) and Ig protease categories in the colon, along with a noteworthy decrease in the relative abundance of plasmid categories in mobile genetic elements (MGEs). Further we examined VFs in feces using absolute quantification. The results showed that high-fiber diets reduce fecal excretion of VFs and that this effect is strongly influenced by MGEs and short-chain fatty acids (SCFAs). In vitro fermentation experiments confirmed that acetic acid (AA) led to a decrease in the relative abundance of VFs (p < 0.1). In conclusion, our findings reveal for the first time how fiber diet and genetic factors affect the distribution of VFs in pig colon contents and feces and their driving factors. This information provides valuable reference data to further improve food safety and animal health.},
}

@article {pmid38689099,
year = {2024},
author = {Agustinho, DP and Fu, Y and Menon, VK and Metcalf, GA and Treangen, TJ and Sedlazeck, FJ},
title = {Unveiling microbial diversity: harnessing long-read sequencing technology.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {38689099},
issn = {1548-7105},
support = {1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; III-2239114//National Science Foundation (NSF)/ ; EF-2126387//National Science Foundation (NSF)/ ; III-2239114//National Science Foundation (NSF)/ ; },
abstract = {Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.},
}

@article {pmid38688217,
year = {2024},
author = {Zhang, D and Li, H and Yang, Q and Xu, Y},
title = {Microbial-mediated conversion of soil organic carbon co-regulates the evolution of antibiotic resistance.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134404},
doi = {10.1016/j.jhazmat.2024.134404},
pmid = {38688217},
issn = {1873-3336},
abstract = {The influence of organic carbon on the proliferation of antibiotic resistance genes (ARGs) in the soil has been widely documented. However, it is unclear how soil organic carbon (SOC) interacts with the evolution of antibiotic resistance in bacteria. Here, we examined the variations in ARGs abundance during SOC mineralization and explored the microbiological mechanisms and key metabolic pathways involved in their coevolution. The results showed that the SOC mineralization rate was closely correlated with ARGs abundance (p < 0.05). High organic carbon (OC) mineralization was conducive to the occurrence of multidrug resistance genes. For example, multidrug_transporter and mexB increased 2.26 and 7.83 times from the initial level. The competitor (stress) evolutionary strategy model revealed that higher OC inputs drive environmental microorganisms to evolve from stress tolerant to high resistance and strong adaptation. Meta-genomic and transcriptomic analyses revealed that the conversion process of pyruvate to acetyl-CoA to acetate was the critical metabolic pathway for the co-regulation of antibiotic resistance. Gene deletion validation trials have demonstrated that the key functional genes (ackA and pta) involved in this process can modulate the development of vancomycin and multidrug resistance. This outcome provides a preliminary framework for microbial mechanisms that target the co-regulation of microbial OC conversion and the evolution of antibiotic resistance.},
}

@article {pmid38687787,
year = {2024},
author = {Kobayashi, D and Inoue, Y and Suzuki, R and Matsuda, M and Shimoda, H and Faizah, AN and Kaku, Y and Ishijima, K and Kuroda, Y and Tatemoto, K and Virhuez-Mendoza, M and Harada, M and Nishino, A and Inumaru, M and Yonemitsu, K and Kuwata, R and Takano, A and Watanabe, M and Higa, Y and Sawabe, K and Maeda, K and Isawa, H},
title = {Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {19},
pages = {e2319400121},
doi = {10.1073/pnas.2319400121},
pmid = {38687787},
issn = {1091-6490},
support = {JP18fk0108067//Japan Agency for Medical Research and Development (AMED)/ ; JP19fk0108097//Japan Agency for Medical Research and Development (AMED)/ ; JP20wm0225009//Japan Agency for Medical Research and Development (AMED)/ ; JP21fk0108613//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108123//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108634//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108625//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108656//Japan Agency for Medical Research and Development (AMED)/ ; Strategic International Collaborative Research Program (SICORP)//MEXT | Japan Science and Technology Agency (JST)/ ; 20KC1001//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; 21KA1003//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; JP18H02856//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20K15671//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Metagenomics/methods ; Japan/epidemiology ; *Deer/virology ; *Flavivirus/genetics/isolation & purification/classification ; *Ticks/virology ; Phylogeny ; Virome/genetics ; Virion/genetics ; Sus scrofa/virology ; High-Throughput Nucleotide Sequencing ; Humans ; Seroepidemiologic Studies ; Genome, Viral ; },
abstract = {During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.},
}

Animals
*Metagenomics/methods
Japan/epidemiology
*Deer/virology
*Flavivirus/genetics/isolation & purification/classification
*Ticks/virology
Phylogeny
Virome/genetics
Virion/genetics
Sus scrofa/virology
High-Throughput Nucleotide Sequencing
Humans
Seroepidemiologic Studies
Genome, Viral

@article {pmid38687700,
year = {2024},
author = {Kimemia, BB and Musila, L and Langat, S and Odoyo, E and Cinkovich, S and Abuom, D and Yalwala, S and Khamadi, S and Johnson, J and Garges, E and Ojwang, E and Eyase, F},
title = {Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0296597},
doi = {10.1371/journal.pone.0296597},
pmid = {38687700},
issn = {1932-6203},
mesh = {Kenya ; Animals ; *Metagenomics/methods ; *Ticks/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation & purification/classification ; Humans ; Phylogeny ; },
abstract = {Ticks are arachnid ectoparasites that rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to the paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with a monsoon climate in the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of the Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naïve Bayes classifier was used to classify the Operational Taxonomic Units (OTUs) taxonomically. The bacteria of clinical interest detected in pooled tick assays were as follows: Rickettsia spp. 59.43% of pools, Coxiella burnetii 37.88%, Proteus mirabilis 5.08%, Cutibacterium acnes 6.08%, and Corynebacterium ulcerans 2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections, and diphtheria-like infections in humans, respectively. P. mirabilis, C. acnes, and C. ulcerans were detected only in Isiolo. Additionally, COI sequences allowed for the identification of Rickettsia and Coxiella species to strain levels in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection of C. acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.},
}

Kenya
Animals
*Metagenomics/methods
*Ticks/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/isolation & purification/classification
Humans
Phylogeny

@article {pmid38687074,
year = {2024},
author = {Ye, J and Huang, K and Xu, Y and Chen, N and Tu, Y and Huang, J and Shao, L and Kong, W and Zhao, D and Xie, Y},
title = {Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0002624},
doi = {10.1128/spectrum.00026-24},
pmid = {38687074},
issn = {2165-0497},
abstract = {The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.},
}

@article {pmid38687069,
year = {2024},
author = {Ma, G and Yan, H and Tye, KD and Tang, X and Luo, H and Li, Z and Xiao, X},
title = {Effect of probiotic administration during pregnancy on the functional diversity of the gut microbiota in healthy pregnant women.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0041324},
doi = {10.1128/spectrum.00413-24},
pmid = {38687069},
issn = {2165-0497},
abstract = {UNLABELLED: Our study aims to investigate the impact of probiotic consumption during pregnancy on gut microbiota functional diversity in healthy pregnant women. Thirty-two pregnant women were randomly assigned to two groups. The probiotic group (PG) consisted of pregnant women who consumed triple viable Bifidobacterium longum, Lactobacillus delbrueckii bulgaricus, and Streptococcus thermophilus tablets from the 32nd week of pregnancy until delivery. The functional profiles of the gut microbiota were predicted through high-throughput 16S rRNA sequencing results using PICRUSt software and referencing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In the gut microbiota of the PG, the genera Blautia and Ruminococcus, as well as the species Subdoligranulum, showed significantly higher relative abundances compared to the control group (CG) (P < 0.05). At Level 1 of the KEGG signaling pathways, there was a significant reduction in the functional genes of the gut microbiota involved in Organismal Systems in the PG (P < 0.05). In Level 2 of the KEGG signaling pathways, there was a significant reduction in the functional genes of the gut microbiota involved in Infectious Disease in the PG (P < 0.05). In Level 3 of the KEGG signaling pathways, the PG exhibited a significant increase in the functional genes of the gut microbiota involved in ABC transporters, Oxidative phosphorylation, Folate biosynthesis, and Biotin metabolism (P < 0.05). The CG showed a significant increase in the functional genes related to Cysteine and methionine metabolism, Vitamin B6 metabolism, Tuberculosis, and Vibrio cholerae pathogenic cycle (P < 0.05). In conclusion, our findings suggest that probiotic supplementation during pregnancy has a significant impact on functional metabolism in healthy pregnant women.

IMPORTANCE: Probiotics are considered beneficial to human health. There is limited understanding of how probiotic consumption during pregnancy affects the functional diversity of the gut microbiota. The aim of our study is to investigate the impact of probiotic consumption during pregnancy on the functional diversity of the gut microbiota. Our findings suggest that probiotic supplementation during pregnancy has a significant impact on functional metabolism. This could potentially open up new avenues for preventing various pregnancy-related complications. This also provides new insights into the effects of probiotic consumption during pregnancy on the gut microbiota and offers a convenient method for exploring the potential mechanisms underlying the impact of probiotics on the gut microbiota of pregnant women.},
}

@article {pmid38687063,
year = {2024},
author = {Chen, Z and Grim, CJ and Ramachandran, P and Meng, J},
title = {Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0011724},
doi = {10.1128/spectrum.00117-24},
pmid = {38687063},
issn = {2165-0497},
abstract = {Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs). This study aimed to assess the potential of long-read assembly algorithms in Oxford Nanopore sequencing to enhance the MAG-based identification of bacterial pathogens using both simulated and mock communities. Simulated communities were generated to mimic those on fresh spinach and in surface water. Long reads were produced using R9.4.1+SQK-LSK109 and R10.4 + SQK-LSK112, with 0.5, 1, and 2 million reads. The simulated bacterial communities included multidrug-resistant Salmonella enterica serotypes Heidelberg, Montevideo, and Typhimurium in the fresh spinach community individually or in combination, as well as multidrug-resistant Pseudomonas aeruginosa in the surface water community. Real data sets of the ZymoBIOMICS HMW DNA Standard were also studied. A bioinformatic pipeline (MAGenie, freely available at https://github.com/jackchen129/MAGenie) that combines metagenome assembly, taxonomic classification, and sequence extraction was developed to reconstruct draft MAGs from metagenome assemblies. Five assemblers were evaluated based on a series of genomic analyses. Overall, Flye outperformed the other assemblers, followed by Shasta, Raven, and Unicycler, while Canu performed least effectively. In some instances, the extracted sequences resulted in draft MAGs and provided the locations and structures of antimicrobial resistance genes and mobile genetic elements. Our study showcases the viability of utilizing the extracted sequences for precise phylogenetic inference, as demonstrated by the consistent alignment of phylogenetic topology between the reference genome and the extracted sequences. R9.4.1+SQK-LSK109 was more effective in most cases than R10.4+SQK-LSK112, and greater sequencing depths generally led to more accurate results.IMPORTANCEBy examining diverse bacterial communities, particularly those housing multiple Salmonella enterica serotypes, this study holds significance in uncovering the potential of long-read assembly algorithms to improve metagenome-assembled genome (MAG)-based pathogen identification through Oxford Nanopore sequencing. Our research demonstrates that long-read assembly stands out as a promising avenue for boosting precision in MAG-based pathogen identification, thus advancing the development of more robust surveillance measures. The findings also support ongoing endeavors to fine-tune a bioinformatic pipeline for accurate pathogen identification within complex metagenomic samples.},
}

@article {pmid38686914,
year = {2024},
author = {Spatola Rossi, T and Gallia, M and Erijman, L and Figuerola, E},
title = {Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/09593330.2024.2343797},
pmid = {38686914},
issn = {1479-487X},
abstract = {Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.},
}

@article {pmid38686909,
year = {2023},
author = {Liu, BY and Zhang, D and Fan, Z and Jin, JJ and Li, CH and Guo, RN and Li, XJ and Huang, Y},
title = {Role of Clinical Features, Pathogenic and Etiological Characteristics of Community-acquired Pneumonia with Type 2 Diabetes Mellitus in Early Diagnosis.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {e221123223715},
doi = {10.2174/0118715303273741231117060753},
pmid = {38686909},
issn = {2212-3873},
abstract = {OBJECTIVE: To study the etiological characteristics of community-acquired pneumonia (CAP) combined with type 2 diabetes (T2D), providing a reference for early clinical diagnosis and treatment of the disease.

METHODS: We selected a total of 93 patients with CAP and analyzed their metagenomics nextgeneration sequencing (mNGS) data. The case group comprised 46 patients with combined CAP/T2D, and the control group comprised 47 patients without diabetes. We analyzed the pathogenic findings of the two groups.

RESULTS: There were statistically significant differences in age between the two groups (P = 0.001). Leukocytes (P = 0.012), blood platelets (P = 0.034), fibrinogen (P = 0.037), D-dimer (P = 0.000), calcitonin ogen (P = 0.015), ultrasensitive C-reactive protein or C-reactive protein (CRP) (P = 0.000), serum amyloid A (P = 0.000), and erythrocyte sedimentation rate (P = 0.003) were higher in the case group than in the control group. Albumin was lower in the case group than in the control group. All differences were statistically significant. The infection rates of Klebsiella pneumoniae (P = 0.030), Pseudomonas aeruginosa (P = 0.043), and Candida albicans (P = 0.032) were significantly different between the two groups.

CONCLUSION: Compared with those without diabetes, the infection rates of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans were higher in patients with combined CAP/T2D.},
}

@article {pmid38686450,
year = {2024},
author = {Marchi, E and Hinks, TSC and Richardson, M and Khalfaoui, L and Symon, FA and Rajasekar, P and Clifford, R and Hargadon, B and Austin, CD and MacIsaac, JL and Kobor, MS and Siddiqui, S and Mar, JS and Arron, JR and Choy, DF and Bradding, P},
title = {The effects of inhaled corticosteroids on healthy airways.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16146},
pmid = {38686450},
issn = {1398-9995},
support = {211050/Z/18/z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: The effects of inhaled corticosteroids (ICS) on healthy airways are poorly defined.

OBJECTIVES: To delineate the effects of ICS on gene expression in healthy airways, without confounding caused by changes in disease-related genes and disease-related alterations in ICS responsiveness.

METHODS: Randomized open-label bronchoscopy study of high-dose ICS therapy in 30 healthy adult volunteers randomized 2:1 to (i) fluticasone propionate 500 mcg bd daily or (ii) no treatment, for 4 weeks. Laboratory staff were blinded to allocation. Biopsies and brushings were analysed by immunohistochemistry, bulk RNA sequencing, DNA methylation array and metagenomics.

RESULTS: ICS induced small between-group differences in blood and lamina propria eosinophil numbers, but not in other immunopathological features, blood neutrophils, FeNO, FEV1, microbiome or DNA methylation. ICS treatment upregulated 72 genes in brushings and 53 genes in biopsies, and downregulated 82 genes in brushings and 416 genes in biopsies. The most downregulated genes in both tissues were canonical markers of type-2 inflammation (FCER1A, CPA3, IL33, CLEC10A, SERPINB10 and CCR5), T cell-mediated adaptive immunity (TARP, TRBC1, TRBC2, PTPN22, TRAC, CD2, CD8A, HLA-DQB2, CD96, PTPN7), B-cell immunity (CD20, immunoglobulin heavy and light chains) and innate immunity, including CD48, Hobit, RANTES, Langerin and GFI1. An IL-17-dependent gene signature was not upregulated by ICS.

CONCLUSIONS: In healthy airways, 4-week ICS exposure reduces gene expression related to both innate and adaptive immunity, and reduces markers of type-2 inflammation. This implies that homeostasis in health involves tonic type-2 signalling in the airway mucosa, which is exquisitely sensitive to ICS.},
}

@article {pmid38686438,
year = {2024},
author = {White, KH and Keepers, K and Kane, N and Lendemer, JC},
title = {Discovery of new genomic configuration of mating-type loci in the largest lineage of lichen-forming-fungi.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae094},
pmid = {38686438},
issn = {1759-6653},
abstract = {The genetic architecture of mating-type loci in lichen-forming fungi has been characterized in very few taxa. Despite the limited data, and in contrast to all other major fungal lineages, arrangements that have both mating-type alleles in a single haploid genome have been hypothesized to be absent from the largest lineage of lichen-forming fungi, the Lecanoromycetes. We report the discovery of both mating-type alleles from the haploid genomes of three species within this group. Our results demonstrate that Lecanoromycetes are not an outlier among Ascomycetes.},
}

@article {pmid38686186,
year = {2024},
author = {Chen, Q and Huang, X and Zhang, H and Jiang, X and Zeng, X and Li, W and Su, H and Chen, Y and Lin, F and Li, M and Gu, X and Jin, H and Wang, R and Diao, D and Wang, W and Li, J and Wei, S and Zhang, W and Liu, W and Huang, Z and Deng, Y and Luo, W and Liu, Z and Zhang, B},
title = {Characterization of tongue coating microbiome from patients with colorectal cancer.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2344278},
pmid = {38686186},
issn = {2000-2297},
abstract = {BACKGROUND: Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC).

METHODS: Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model.

RESULTS: We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as Atopobium rimae, Streptococcus sanguinis, and Prevotella oris aided differentiation of CRC patients from healthy participants.

CONCLUSION: These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.},
}